You can structure it pretty much however you want. Download a file manager from the market so you can navigate around, pretty much like a pc. Personally I like Linda File Manager, but others like IO.
As for transferring files, have you heard of DropBox? It allows you to keep a folder on multiple PCs that automatically syncs and is accessible through the cloud. They have an Android app as well. Pretty freaking awesome if you ask me!
Standard free account is 2gb but if you click my referral link here then we BOTH get an extra 250mb.
http://www.dropbox.com/referrals/NTEzMjg4OTgwOQ
Another alternative (but only uni-directional, not bi-directional) is Awesome Drop, also available in the market. This allows you to use a web browser to drop whatever file you want directly to your phone through the 3G, no cables required. Pretty sweet, but DropBox is better in my opinion.
Check em all out.
EDIT - here are some links for you.
Linda File Manager
http://www.appbrain.com/app/linda-file-manager/com.lindaandny.lindamanager
DropBox App
http://www.appbrain.com/app/dropbox/com.dropbox.android
Awesome Drop
http://www.appbrain.com/app/awesome-drop-%28file-sync%29/com.dashwire.drop