From what I've read I don't think this is possible. You can set the target folder from the report properties as you've already discovered. And it's possible to have multiple configurations set up (eg I have my Debug profile publish to all the reports to an In Progress folder that only I have access to and my Production profile publishes all the reports to the public folder). But from what I can gather it's not possible to publish reports to multiple folders from within a single project.
I've dealt with this by having separate projects for different groups - a Rent Accounting project, a General Management project, a Maintenance project etc. But this doesn't allow for any fine control over report destination and I still have to manually move some of the reports after deploying.
Hope this helps,