Get a test disc with 1K tones at 0, -5, -10 dB reference levels. For pure SQ use 0 or -5, for everyday systems use -10 dB. Turn all gains down (amps, eqs, crossovers etc). Play the test tone and put it on repeat. Turn up the deck until you hear the tone change, it will be clearly audible, then once it changes turn it back a click or two (alot of decks won't clip so just keep the volume at max then). Proceed to the next component in the signal chain (eg. eq) and turn up it's gain until you hear the tone change again. Turn it back a click or two. And so on down the signal chain until you get to the amps. I usually turn down any sub amps or such to match the rest of the amps levels, you might have to turn the mid amp down to match the subs, the point being just turn amps down to match between subs and mids, never bring an amp up to match at this point.

 

It can get loud in the car, but it should be tolerable for a minute or two, if your amps are in the trunk I recomend making sure you are quick to adjust the amps. I don't like to have high output tones through my speakers for more than a couple minutes at a time.

Also make sure your bass and treble are flat, and keep any eq or anything off as well, then don't vary it too much when using the deck.