Mbox issue-not an Mbox user so I can't offer much, other than, if it sounds good, it IS good(IOW, don't worry about where the knob points, as long as you have the required/desired signal, which ideally would be just into the yellow on the track meter). BTW, keep the metering in Pre-fade mode for tracking
ProTools issues-to bounce the desired amount of time, there are several ways to highlight the amount of time you want in the bounce. Mine is to pick any audio track that runs the full length(if this track is a bunch of chopped up clips, I will consolidate it first). I just highlight any audio track that covers the desired time and run the bounce. Another option is to zoom out so the entire project fits on the EDIT screen, drag across any track to select the time you want included in the bounce(quick and easy if you don't mind trimming the head and tail afterwards).
After clicking on a knob or fader, hold the Ctrl key to enter "fine adjust" mode