I don't believe that functionality works yet. I have tried to sideload PDFs and plain .txt files and they don't register in "My Library" or under "My Files" and obviously they don't sync between my devices. I also can't find a web interface for loading non-nook files.
I did a little searching around a couple months ago and I found a few unsubstantiated forum posts that claim that it's planned functionality but the Android app currently only supports sideloaded ePub files.
If not, any ideas how I could accomplish this (other than doing it manually which I currently do)?
I'd say your best bet right now is to do this outside the Nook app. Sideload (or wait till Jan for the Market) a PDF reader and Dropbox or SugarSync onto your Nook Color to keep your PDFs synced and accessable.
*For full disclosure: those Dropbox and SugarSync links are my referral links so if you don't already have them and you use those links both you and I get some free extra storage ;o)