Don't fill in the gaps between the floor boards with ANY type of filler. If you do, and the wood wants to expand, the floor will buckle! Unfortunately, the 'best' way to have prevented this was to have the flooring 'sit' in the house for a week to get acclimated to the house. Constant humidity would be good too. That way, the wood WON'T expand and contract, at least to the naked eye.
As for the staple holes, you can buy pre-tinted filler. Check around. Or, you can buy something that's a shade lighter (or neutral in color) and try to hand-mix in some stain until it matches the stain you're using. Just roll the putty in between your fingers with some stain. Test it along the edges of the room first until you can see the results when the putty dries. Sometimes, you need to go HEAVY with the stain when you roll the putty but it will lighten up a little as it dries. It's not a perfect solution anyway.
The way I look at solving your latter problem is not to try too hard. If you ask people to LOOK at the filler in the staple holes, they'll say it doesn't match. What I say is don't say anything! ANd if they DO see a differenct (on their own), tell them they have too much free time on their hands ...
My best to ya and hope this helps. Forget about filling anything with sawdust. When you go to stain and finish the floor, you want it as COMPLETELY dust and dirt-free as possible! (I don't know if the one store employee has a 'clue' as to what he's talking about ...)