If you dont have a master recorder, like a masterlink or tascam (or 2 track tape

), then you probably want to go back into the MOTU after mixing on the board like you mentioned, to utilize your mastering plugins. and even if you DID have a master recorder, you still might want to go back in the box to use plugs, assuming you dont have any decent outboard mastering gear.
you will hear from many on this board about making multiple passes through converters and its potential to degrade signals. I will also agree with that, so I try and keep the AD/DA passes to a minimum.
I have a similar setup. I use a MOTU 24 i/o, and I track everything through a Soundtracs Topaz 24 channel console then into the 24 i/o. i edit in the box, using DP and PT, then back out again to mix on the board. i have a couple comps for the mix bus for my topaz, and a Masterlink to mixdown to. Ill leave the REAL mastering to a masterhouse from then on out, unless im in a pinch. I can bring the track back into the box from the masterlink to use some Mastering plug ins.
Sounds like you have some nice plug ins, so you should play around with doing more out of the box vs. more ITB, and see what you prefer.