I worked on a documentary with a similar issue. All I can offer is what I did:
1. Bring them in exactly as you wish them to look in the final project. Don’t assume your AE artist will know what has to be pillarboxed, stretched, etc. It’s a lot of work, but you will save yourself headaches later on.
2. Keep color spaces consistent. On my show, we worked with a lot of photos from the 80’s and 90’s. In the offline, they looked fine, but in the online we found that they were in CMYK. It gave them a sickly greenish tint in hi-res. If you can, bring them all into photoshop and export in RGB (I may be talking out of my ass here – I didn’t have to do that part).
3. Are you working on a Unity? If so, when you link via Pan and Zoom, keep all the photos on the desktop in a generic folder (i.e., Episode 1 Photos). Link to that. When you bring them into the online, copy that folder onto the desktop. They should all re-link. If you link them from a Unity, keep in mind that sometimes those drive letters change. If that happens, you’re stuck re-linking everything (Avid was looking for them on Drive H, for example, but now Drive H is Drive R). The C drive, however, is always the C drive.
Hope that helps a little.