A few items...

1. This had nothing to do with running with administrative rights (terminology overload because it was telling you to use the webapp administrator to stop the webapp)
2. There is no need to run the Studio with elevated rights (as administrator) - in fact, it's a really bad idea to do so because you could be courting problems with virtualization of files and registry entries.
3. As others have mentioned, if you are going to be making any changes to the underlying database, you must stop the webapp first because webapps always keep tables open and the Studio needs to open tables exclusively to make changes.