yeah...i was thinking maybe for some reason google play would need to know where the files are stored locally just for a second or something. guess that doesnt make too much sense
When you upload files using the Google Music Manager, you're selecting a location on your computer for the Music Manager to watch, rather than to upload files from on a one-time basis. If you change the contents of that directory, it should be reflected in Google Music. I can't say exactly how it handles files that have been deleted or are no longer present in that location, because I've had varying results.
Edit: I should mention that as of an update to the Music Manager, there is now a boolean option titled "Automatically upload songs added to my selected folders." I do believe this is checked by default. Then there's the option to start at boot. Here's what I would do:
1) Turn off the automatic upload.
2) Turn off start at boot.
3) Upload your entire library once, keeping in mind that it may take multiple passes to get everything pulled up.
4) When you want to update Google Music, manually start the Music Manager and scan for the new files.
This is how I do it. When I add new music, I create a new folder (so my library -- on an external hard drive -- contains folders for each date that I added new music to Google Music). I then have Music Manager scan and upload that new folder. Once the files are in Google Music, that folder name has no significance and the tracks are organized/sorted as they would be normally (title, artist, album, etc.).