Yes, I would generally do it this way - set the amp "flat" and do all my EQ using the preamp. Because excessively boosting on one and cutting on the other isn't doing anything to help make sense of it all (and probably introducing noise and filtering issues.)
But doing it that way, you can get "your sound" on the preamp (mark those settings) and if there is an issue at a particular venue that is causing problems (boomy stage, bad slapback) that you have to use EQ to dial out, you do that on the amp. At the end of the gig, you reset the amp to "flat" and you're back to your starting point.
Or, if you like what the preamp does, you jack into the "effects return" on the amp (if so equipped) which should essentially bypass almost the entire front end of the amp, turning it essentially into a powered speaker. That's another option. Then you have a "specially designed for acoustic" preamp, and no significant additional interference in its tone.