"Best" application will depend
Might be a rag, might be a brush....
Originally Posted by slickshift
Your application technique will vary depending on the wood (which varies in color and absorption even in each piece) and color/type of stain
You need to try a few different techniques on scraps (or in a non-obvious area) to be sure it's even close
It may just be a wipe-on/wipe-off affair, or it may be a multi-coat, or even multi-color, job
It may be a one-coat...leave for 5 minutes, wipe-off deal...
Stains are simply not like paints where there is any one answer, and they are most difficult to "match"
Hopefully, your stain is pretty close to what you need, and a simple technique will get it close enough
As for poly, the best tools will get the best results
I'd recommend a quality white china bristle brush