It depends on if you're a "hands on" audio guy or not. You've got it set up in one correct way, but to mess with it you'll obviously have to adjust the amps themselves. Hopefully not while your driving

.
If you want to mess with them while you're driving you'll want to set everything up with your head unit. I, perhaps shamefully, like to sit in my truck quite often to listen to music, so I like to be able to play with it on the head unit. My head unit though has quite a few adjustable options. If your new one doesn't have as much flexibility, then set it and forget it. As time goes on, you might decide you hear something you don't like, and you'll want to play with it on the deck. It's not usually a good idea to use both the amps and the head unit to make crossover adjustments, but if you know what you're doing, you can use it as another tool in your tool box.
Crossover tweaking is large scale sound shaping, while EQ is fine tuning. Don't get caught up messing with the crossover when what you're looking for is EQ.