stain with brush and wipe off with clean rag after giving a few min for the stain to penetrate the wood. if it is too light when you wipe it off let it sit longer before you wipe off the excess
let dry for a minimum of 24 hours this is very important for oil based stains. when stain dries it releases gas. if you poly over it too soon you will get bubbles in your finish
apply first coat of either polyurethane or sanding sealer
sand and wipe with tack rag or thinner rag
apply 2nd coat of polyurethane
you are done. you can sand and apply a 3rd coat if you like
NOTE: i fill my nail holes after my first coat of clear. i use a colored nail hole filler. if you fill the nail holes before the wood has a clear coat the tinted nail hole filler can make a darker area on the wood where you rubbed it in.
If you are using latex stain and Polycrylic the system is the same but dry times are much quicker. read the labels on all products you are using.