Your link doesn’t work for me, sorry. Could you place a space on each side of the URL?
As for your problem, I’m not sure I understand, but here goes: Do not change any layers in your composition. Lock them all. The only thing you should change is the start and end of the work area (check the help).
Yes, if you render to a numbered PNG sequence, you can render in sections. Once you’re done, import the rendered sequence into AE, and drag it onto the new comp button at the bottom of the project window to make a comp. For audio, I’ll leave it up to you as to how to get the desired audio into this comp. Render this comp to a Quicktime movie — it shouldn’t take as much RAM given that you’re just rendering frames with no effects, no multiple layers.