I would suggest two coats of stain, sanding between each coat with a light grit sandpaper (220 or above). This will rough up the surface a bit and take care of any debris that may have been on the floor. A good method is to wipe the stain on w/ one rag, let is sit for a few minutes, then blend it together w/ al clean dry rag. Make sure you vacuum the floor, then go over it with a wet towel to remove anything left behind. Don't forget to vacuum the baseboard and 3 feet up the wall to remove any dust. Also, I would suggest at least 2 coats of poly, and 3 in heavy traffic areas. Use a satin poly, this will hide any mistakes or imperfections. It is very forgiving. Don't forget that after you poly, the stain will look 10 times better!
We just finished our wood floors, 900 SQ FT! This is the method we used and they turned out beautiful!