Can I run a Pre/Pro thru a Pre-Amp without by-pass

Nope, like Lazarus said you just need to be able to set the 2ch preamp's volume control to an easily repeatable position, like 12 o'clock, each time you use the pre/pro.

You would just adjust the volume on the pre/pro? Even without a HT-bypass, just set the analog preamp to a repeatable position, then adjust the levels of the L+R relative to center+rears on the pre/pro. Then anytime you need to adjust movie volumes you track at 5+ channels using the volume pot on the pre/pro, only. Not the preamp. It remains at the repeatable, fixed volume for the entire movie regardless of volume adjustments to the pre/pro.