I have all my outboard on my MixBay with (2) Lynx Aurora16's hooked into a PT|HD3 Accel rig. I've normalled all the gear that I use every mix and set all of that up in the i/o section of PT and then I patch in whatever I need additionally as well as create outboard gear chains as needed. Works amazingly well and is full delay compensated. I've actually done quite a few A/B comparisons between the actual gear and their plug-in emulations and I can tell you without a doubt the actual gear always wins. This is not to say there aren't any good/worthwhile plugs, there certainly are (McDSP and SoundToys immediately come to mind), but if you've got the real deal hardware and can use it all while still mixing ITB it's a fantastic outcome.
For recall settings I use the notes section of each track in PT and write down everything. This way it's there for me, saved with the session. I can recall a mix within 15/20 minutes max because of my detailed notes.
I too work in Pro Tools with outboard gear. According to what Kittonian said (which is exactly the same way I do it) once you have all the outboard gear connected to the I/O interfaces you just create an I/O template labeling each connection with the names of the corresponding outboard processors. They come up in your insert points in Pro Tools tracks and auxes, so that's actually your patch bay. You just treat them like you would insert plug ins. Works like a charm.
I add a compressor on the return form my summing output (it can be tube or solid state, depending on the song). I don't have that ton of outboard (unfortunately...but it's growing fast ), so I just write the settings for each processor on the comment section of the PT track, and manually set them. I find that since I tend to use the same processors on kind of the same sources the settings vary slightly (if at all sometimes), so recalls aren't that big of a deal. Digital units get the preset stored and recalled instantly.