From whence are they fed? Where will you put your interlock?
I happen to have a superficially (since I know no details of yours, yet) similar setup - mine is fed from one meter that feeds both panels. I dread to think what it would cost to put a transfer switch on that feed line, so each panel has an interlock and generator input. My reasoning is that I want to be able to power any circuit without any unsafe power outage creative wiring, but not all at the same time (that would be a BIG generator and the cost of that is also outrageous.)
Most of the time only one panel (in my setup) will need a generator attached to it, but the input is there on the other panel in case I wanted to power one of its circuits in the event of an outage - to avoid unsafe power outage creative wiring. Unless I got crazy and got two generators, I'd expect to power down the one panel and move the generator cord to the other one, rather than trying to power things on both panels at the same time. The "primary" panel in that sense is the one with the well pump and most lighting circuits on it. Refrigeration will also end up there, by design. Load control is by hand, but it's much nicer to be able to have well water (and turn the fridge and some lights off while getting it) than to haul water in a bucket from a stream.
I'm dubious about trying to feed from one generator into both panels at the same time, but if you have a large enough generator (and enough output breakers switched off) and sufficient hardware it should be possible, it's just not something that I personally looked into in any detail, as I had the thought in mind that I'd land loads I might want on a generator mostly on the one panel, but spend the small amount on an interlock for the other panel as well. I don't know if you'd have to have a sub-panel from the generator input to split to the interlock inputs, or if you could just depend on the generator output breaker at one end and each interlock breaker at the other end, with no more hardware needed in-between. Given how interlocks work, I can't see any unsafe condition arising from two interlocks on the two panels (i.e. you don't appear to be asking about "backfeeding from a sub-panel" which you cannot do.)
Depending what your reasoning (and scale of generator) is, you could possibly move circuits you expect to need to power from a generator all to one panel.
Ok you wrote a book. Proposing all manner of third rate hackery. And what does it boil down to? You want to get 5000W out of your 5000W generator. Quick question.
What is 240 x 21 ?
By my math, it's 5040. There's your 5000W. You do get it out of the big NEMA L14-20 connector.
I have no idea where you got 41A. I'm pretty sure you made that up, probably by dividing 5000 by 120. I seriously doubt it was on the generator spec. There's a way if you really really want that, but as you get educated, you will realize you do not.
What is it you're missing? The odd idiom of North American 2-pole service. I don't blame you for not getting it... It's weird.
Your house is served by +120V, neutral (0V), and -120V. I just described an instant in time, they're AC so they will reverse position 120 times a second. The poles are called L1 and L2 and the middle is Neutral.
240V loads grab L1 and L2. 120V loads grab either pole and neutral. Which pole they grab is nearly random and that's the idea, to make them average out so loads are balanced.
For you, with 21A on each pole, balancing is a big deal. You'll have a problem if you put 30A of load on one pole. So you'll need to get into the gory details of what is on which pole, and manage accordingly.
Step 1: Control MWBCs so they don't kill you
I don't recommend rearranging things on a panel because you can break a type of wiring called a multi-wire branch circuit. Find an electrician and tell him to do exactly this:
find every multi-wire branch circuit in my home, and make sure both its hot wires are served from the same 2-pole breaker.
Step 2: get rid of double-stuff breakers
If your panel is stuffed, and has lots of breakers that have 2 breakers in 1 space, those will drive you absolutely bat crazy. ack... You know what, to heck with all that.
Let's just get you a new subpanel with the appropriate interlocks, and move the loads you want the generator to power into this new subpanel. Make this subpanel quite large (at least 20 space) realizing you'll use 4 spaces just for the interlock.
In a perfect world, your new panel will have ammeters which will tell you how close to 21A each pole is getting. Even better get one of those new fangled whole house monitoring systems. Ask a new question on how to get one to work in a generator interlocked panel.
Step 3: rearrange your loads in the panel
Now finally, it's time to learn the gory details of how poles are assigned in a panel. Read my posting here. Your panel may differ, but probably not by much.
Move your loads into the new panel, and consciously and carefully balance the loads. For instance if your table saw is on L1, put your dust collector on L2. Stuff like that.
Best Answer
The 4 Rules of Standby Generator Hookups
There are four rules that must be followed in order to have a safe and Code-compliant generator hookup:
It appears that you have 1 and 2 taken care of, and 3 is not hard (just use the proper inlet box if you don't already have one, it's not that hard to find), but point 4 is where your plans are running aground, in more ways than one.
There Can Only Be One (Neutral-to-Ground Bond)
One of the fundamental rules of grounding is that there must be one, and only one, place in a typical building's electrical system where neutral and ground are connected, or bonded, together. In most houses and other light-duty buildings, this is done in the main panel; as a result of this, most main breaker panels, yours included, are shipped with their bonding means factory-fitted, and futhermore lack separate ground bars.
As a result of this, both wires can be connected to the same bar, right? Well...it's not that simple. You see, your main panel provides a neutral-to-ground bond for your house, as it should. However, your generator also bonds neutral to ground (aka the frame), so that it can provide a properly bonded electrical system when it's being used as a standalone power source, such as on a jobsite.
This leaves us with two options for dealing with the problem. You can either
Remove the generator's neutral-to-ground bond, or
Set up your standby system for a bonded neutral generator.
We'll cover removing the generator's bond wire first, as that's the more practical option in your case.
Afloat in a sea of neutrals
The first option is to remove the generator's neutral-to-ground bond, thus making your generator a floating neutral generator. This makes the generator less useful for portable use (as you'll then have to have a way of supplying the neutral-to-ground bond when using it as a portable generator, such as through a L14-30P with a 10AWG wire jumpering N to G that is then plugged into the generator's L14-30R when used as a portable), but would let you use it with your interlock setup (the correct interlock for your panel is a HOMCGK2C, by the way) with no further ado.
The downside here is that you'll need to have your generator spend some quality time with a qualified generator serviceperson for this to happen, as your generator's manual provides neither a wiring diagram nor a procedure for removing the N-G bond for standby usage, and technical support was of no use in that regard either. Of course, you could return it and get a generator that provides better support for such usage, for that matter.
Giving the neutral the switcheroo
The other option you have is to set up your standby system so that it can work with generators with bonded neutrals. However, this requires switching the standby neutral between utility and generator power, so that the standby loads are only connected to one neutral-ground bond at any given time. This is something ordinary breaker interlocks cannot do, as ordinary circuit breakers don't switch the neutral; in fact, there is no such thing as a switching neutral breaker in Square-D Homeline, never mind that Square-D simply does not make a main breaker which switches the neutral wire.
As a result, you'd need to use a separate transfer panel for this route; the XRC0303D (now replaced by the XRK0303D) from the Reliance Panel/Link X series is probably the simplest choice for your application if you want to go down that road, as you can simply transplant your existing Homeline breakers into it for the circuits you wish on generator power. It does require some rewiring (using a fat nipple between the two panel enclosures and a bunch of THHN to route circuits between the two panels), but would let you use your existing generator, or really any portable generator of suitable wattage, in its factory-stock/unmodified configuration.