presets.xml is the way to setup the dashboard for new users. Check out the "user-dashboard" part of it, then extend it (so it doesn't get overridden if you upgrade alfresco).
As for existing users, you should use share sitestore directly - I think you can access it from repo console. You should go into each of the users' existing xml presets and change them and stuff, but that part is very tricky, so test it a lot first, I suggest.
Maybe there is a better way, but I don't know it.