First, a quick note on technique - start with a coarse grade sandpaper on the floor sander and work down to the the finer grade.
The coarse grade removes the old finish and levels out the imperfections, then the fine grade makes it nice and smooth. If you go the other way around, you'll definitely curse every time you see the grooves in the sunlight. Fixing this means stripping off the nice new finish, not fun.
In passing, an obvious-in-hindsight but sometimes-missed point is to go with the grain, i.e. sand along the boards, not across them. In any case your sander will complain bitterly if you don't.
Also, give the boards an incredibly good wash before you start with e.g. Sugar Soap - you want to try and strip off everything gungy to stop the sandpaper clogging too often. Leave for at least 24 hours to dry nicely.
Be sure to hire an "edge sander" too, this will help you get to the edges that a drum sander won't get to. If you can, remove the skirting boards (baseboards) as then you can get right underneath; only do this if you know you're redecorating the walls too and don't mind patching up the woodwork. You'll inevitably end up doing the fiddly bits around the door frame and right in the corners yourself by hand with a scraper or sandpaper, which takes longer than you could possibly imagine.
While doing the sanding, remove everything from the room (obviously) and get heavyweight dust sheets to tape around the door. Wear airtight goggles as this is an insanely dusty process. You'll also need ear defenders as this is an insanely loud process too.
Regarding stain, it's a matter of personal preference. I've done both and prefer the more uniform result that stain gives.
Regarding finish, I've used both oil-based and water-based finishes. Both are OK, but the oil-based one looked richer (can't say why, can't say how) -- and took about three days to dry. Somewhat inconvenient for a hall, and our puppy left nice pawprints.
Follow the instructions on the tin; in general thinning probably isn't worth it, as you'll find the second and subsequent coats will go further anyway. I applied three coats of the oil-based finish, and five of the water-based finish, but this depends on the state of your boards. It's handy to rent good bright work lights so you can see where you've been, especially for the second and subsequent coats.
What is important is that you get flooring-grade varnish, regular varnish won't stand up to the first party, and yacht varnish will cost so much you won't have the first party...
The finish color is dependent on two things...the stain, and the substrate (well, and some other variables as well...such as application method, length of time before you wipe it, how many coats, etc.). You can't use one stain on two substrates and expect a match anymore than you would expect finding a match with two different stains on one piece of wood.
So, I think the best you can do is stain one using the stain you want, then get scrap wood of the other material and start a trial-and-error process looking for a stain that will result in the match you want.
Alternatively, use the same species of wood for both parts, or consider going for a purposeful contrast between the two woods.
Best Answer
The short answer is that filler isn't commonly used to repair the surface of a wood floor. It may be used to fill gaps between planks where shrinkage has occurred, or to repair holes drilled for wiring, etc., but floors are usually either sanded aggressively to remove all surface damage, or the damage is left as "character".
You may be able to lightly dampen the areas of concern with water to check for remaining filler. Keep sanding until it's gone, then stain and seal the surface.