You could use a subpanel.
I'm assuming you have a series of 120V receptacles on this circuit, at 20A or 15A.
You would keep the 20A 2-pole breaker on the main panel, and the 12/3+G cable.
At the other end, put a very small load center. You can use a "main lug" type, 2-circuit, 4-space. They're under $20. For example: http://www.amazon.com/dp/B000BPOROY/
Then you can put AFCI breakers in this subpanel to branch out as needed.
I haven't gotten a reliable answer as to whether 20A subpanels are allowed in code (30A may be a minimum), but the electrical theory is sound.
You're in conduit, use individual wires - they are cheaper, they pull easier, and the conduit fill on cables is terrible.
Typically we shoot for less than 3% voltage drop at rated current. Less drop is OK.
I'm fairly sure you need 6Ga wire minimum for a 60 Amp feed - given a short 30 foot run, this is also probably perfectly adequate. I'm getting 1.8% drop for 60 amperes at 240V on 30 feet (one way) of 6 Ga. Edit - Copper!
The limiting temperature rating if using THW, THHN, etc wire is generally the temperature rating of the connectors on the service equipment (breaker or panel) which is usually 75 C - even if using 90C wire, you have to follow the 75C section of the table due to the connections.
Copper .vs. Aluminum.
Copper (Cu) costs more, Aluminum (Al) less.
Copper has better conductivity - effect being, smaller wire to carry the same current. In this case, 6 gauge copper .vs. 4 gauge aluminum.
Copper oxides are conductive. Aluminum oxide is an insulator, forms quickly, and sticks very tightly to the wire. Aluminum connections need special procedures and materials to make a solid connection that won't get loose over time and overheat. These include things like brushing the wires with a stainless steel brush and an aluminum wire connection compound that coats the wire to prevent contact with air. The connections themselves must be rated specifically for use with aluminum, but most large ones will be (generally marked Cu-Al meaning they work with both, where unmarked connectors are assumed to be copper wire only.)
Aluminum connections are further complicated by cold flow, but that gets long and complicated to get into, and is supposed to be addressed by using the proper connector types. Essentially the connection gets hot, the wire swells, the swollen wire deforms, the wire shrinks, the connection gets looser, so next time it gets hotter, repeat until fire.
Best Answer
First, get Amps
You start by looking at the instructions on the heater. If the instructions say to use a specific breaker and maybe wire size, then that's what you do, and you're done with this section.
If the instructions don't say, your next stop is the nameplate on the heater. Either literally a nameplate, possibly behind a cover, or in the documentation. You are looking for either
Now derate that Amps number by multiplying it by 1.25 or 125%. That is because it is a continuous load and runs the wires pretty hard.
For instance, if the heater was 30 amps, multiply that by 1.25 and get 37.5.
Now size your breaker and wires
Take your instructions or derated amps number and round UP to the next larger size of 30, 40 or 50. So 37.5 becomes 40.
That will be the size of your circuit and breaker.
You can use larger wires if you really want to. There are some good reasons to do this, like the possibility of upgrading heaters later. But you must stay with the breaker size determined by the need of the heater, as we did above.
Upsizing wire for long distances
Not an issue at 40'.
Over long distances, wires can have "voltage drop". It may be desirable to limit voltage drop by using larger wire than required. First, nobody cares about drops less than 3%, and that happens at around 120' length (round trip) on most wire sizes. So below 120' you never have to worry about it. Otherwise it depends what your loads can tolerate -- resistive heaters are very tolerant of voltage drop for instance; motors not so much.
You usually don't need /3 cable for heaters
/3 cable has an extra conductor, allowing 240V and also a middle neutral, making both 120V and 240V available. Dryers and ranges need this. Water heaters, A/C and electric heaters usually do not. Therefore running /3 cable is a waste of money unless a) the heater says it requires it, or b) you expect in the future to fit something that would require it.
Some people believe that running /3 lets you carry more power. That is not true unless you are dealing in 3-phase "delta", but you won't have that in a residence.