Yes, you probably should generally get into better habits. *But*, for tracks and busses, Logic really doesn't care. Unlike old analog or fixed-point digital devices, there is no distortion penalty for going "over 0dBFS" (or "into the red") internally in Logic, until you hit the outputs, where your nice, high headroom floating point audio is brickwalled to a fixed point format, and anything over 0dBFS is hard clipped.
If you are bouncing your tracks out from the regular outputs, then just lower the output fader by however much quiet your want the tracks, and bounce them. Easy peasy, and you'll know next time that should you fail to be good engineer level dude, it's not a massive problem to deal with...
I must have misunderstood you. I thought I could just use the Gain plugin on the Stereo Output and bounce individual tracks lower that way. That's not working for me, but I just hear the track lower, but the bounce comes out without level reduction.
Edit: Normalise was on on the Bounce window. Yes I am stupid sometimes.