i doubt there is any documentation on the subject per-se. note that the web2py DAL simply translates the web2py style schema definitions and queries into raw GAE datastore queries. if you get really bored and read the DAL you'll see it's just a wrapper around what you already know. you'll also find that there are some GAE features that are not implemented in the DAL yet.
if the web2py models and raw GAE models are all different models there should be no problem. if you are accessing a particular model via GAE and web2py just make sure that the web2py represent and requires are written in such a way that any data that may be inserted by the raw GAE access will not cause them to break. for my largest web2py project (starmakerstudios.com and the associated iphone app that talks to the DB) i do all my day-to-day work with web2py DAL, but schema migrations are often done with raw GAE access. hope that helps. feel free to fire off specific questions. cfh
