I can't say it's good or bad... but mixing my guitars into the practice sessions is what I do. I confess that I've become lazy and do most of my drills (dexterity, scales, chords, etc.) on the electric because it's easier to play and my acoustic six string is used mostly for song practice. Depending on the tune, I occassionally throw in my 12-string. To be sure, different songs benefit from different guitars.

I'm not the one to judge but I see nothing wrong with alternating days between your two guitars. Most certainly, you want to practice on both.

Have fun.