This could probably be summed up in a few words (the words being “use symlinks”).
Basically, what I wanted to do was to sync several folders outside my dropbox folder (for various reasons). The solution was to create a shortcut in the folder I wanted to sync, and then moving the link to my dropbox folder. This can be done of the command line by typing something like:
ln -s /home/folder/to/sync /home/andy/dropbox/synched_folder
This could be used in all sorts of ways, some of which I may blog about over the next couple of weeks.