It all boils down to comfort. Sometimes you only need 3 fingers. There's no use of throwing in an extra finger if it's not needed.

Sometimes I use 3 fingers on some licks, sometimes I use 4, all depends on the lick, the stretch, how many notes.....blah blah.

Just do what's comfortable.

Dream Theater guitarist = John Petrucci

If you're still having problems, just post some licks, I'll/Others will tell you how we play them.