For the duration stuff check this: rd: CompSetter. As for updating your stuff - AE does not retain any structure info on layered PSDs or such (for the msot part simpyl since neither PS nor AI care for providing unique layer IDs that woulkd allow it to begin with). It's just a one time import process with the added convenience of AE organizing it for you, that's all. if you must add more layers, the easiest way would be to import the full document a second time as a composition and then copy&paste the missing layers to the parts you already have done. You can then always delete the redundant duplicates from the import and reorganize your project as needed...
If you add layers to a Photoshop comp they will not update when you reload the footage. Replacing footage may or may not work. The easiest thing to do, other than planning ahead, is to simply rename your photoshop composition, then open it as a composition. Now delete all the layers that you've already animated and then copy all of the layers from the original composition and paste them in the new one or copy only the new layers from your new PSD file and paste them in the existing composition.
When you're finished with your project then you can delete the unused compositions and use the collect files feature to clean out the mess.
I hate to admit that I've had to do this more than once. It only takes a few moments and could have easily been avoided by more carefully planning my composition in the first place.
There's also nothing wrong with simply making a new psd file that contains the required new layers an bringing that in as a separate file.
Amazing Mylenium! A plug-in just a few months old that does exactly what I was looking for, you know if you didn't post here I may have never found an easy solution to that problem. If Adobe doesn't pay you for all the help you give people here they should start!
The script that Mylenium pointed out to you is recommended in the After Effects Help section about composition settings. You'll find that very often the Help document includes such information.