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.
Hope this helps