I've got some very limited experience in the BNF and I'm going back in a few weeks for more. What exactly is it you're looking for? My experience of the online catalog is that, like most other library catalogs, it's much better at finding things when you have some sort of idea what you're looking for, rather than, say, a vague topic. The manuscript department has details of all their manuscripts by call number, which is great if you've got a reference but don't know what it relates too, but not really the other way round.

I haven't used the AN, but if they're like the various archives départementales (and I do think it's a single national classification scheme), then the series are organised by source, into pre- and post-revolution categories. So series G is pre-revolutionary secular church sources, H is pre-revolutionary regular church sources, C (I think) is pre-revolution royal administrative sources. I'm sorry I can't be more specific - if you want to go into a bit more detail about what you want to find I might be able to help more - but whatever it is, good luck!