Well, you know... there are a lot of folks on here who might say "doesn't matter" and, to a large degree probably not too much. That is, until you get on stage, or have to play with a bunch of other guys and can't figure out why your tone isn't working, why it's so bright, how to control feedback, etc...
I firmly believe that you need to get to know your amplifier. It is a major component in your signal chain, and getting used to how it responds to your touch is definitely something I would recommend. Practicing so that you can go out and play, on whatever level is really the end objective, and if nothing else, practicing all of your finger exercises and scales and stuff to a metronome, through an amp is going to amplify every mistake, glitch, brush of the hand against the strings, pick hitting the pickup, etc. It will teach you dynamics, volume control and all sorts of other things. Every amp/guitar has a unique tonal characteristic. Best way to improve your tone is to practice more... My favourite two practice amps are a Peavey Classic 30 and/or a Marshall DSL 401 JCM 200 Combo. Both are absolutely mercilessly unforgiving gain tones hahaha and excellent cleans!
Good luck!