At the moment (May 23, 2013), you can only have one Scala IDE plug-in per Eclipse intallation. Hence, if some of your projects are on Scala 2.9, while others are on Scala 2.10, you will need to use two different Eclipse installations, with the right Scala IDE plug-in installed.
We are aware that this isn't ideal, and we are actively working to remove this limitation.
The best workaround I can offer you at the moment is to use the pre-packaged Scala IDE SDK, which is available for both Scala 2.9 and Scala 2.10. This way you don't have to waste time setting up Eclipse for Scala development.