Chromatics are atonal and therefore won't fit into chord progressions you may be playing over. This means you shouldn't be overusing them. When i want to play a chromatic passage I usually chose a given interval (not too large) of the scale I'm soloing over and I play all the notes in between.
Personally there are only two reasons why I may decide to do this:
1- I want to create a tension feeling when going from the first note of the inteval to the last one by playing all the notes between them, even the ones not in the scale.
2- The extra notes in a chromatic passage may help me to get my timing right. I mean if i want to go from one lick to another and the first one doesn't finish exactly where I want to start the second one, then I may add some chromatics to be sure the second lick is where I want it to be (timewise).
The second point is quite hard to get the hang of, specially when playing fast because you have to be very aware of time. Petrucci uses chromatics a lot because he has a perfect sense of time keeping (which also allows him to play insanely fast).
I hope my poor english was clear enough and of any help.
