For those interested in how to do it, here's the steps:

1. From the Java Perspective right click a file/package and select Team->Synchronize Outgoing Changes
2. To compare the version you're check in with what's in the repository, expand the folders containing the resource you're interested in checking in
3. Double click the resource to open the Java Structure Compare and Java Source Compare
4. Read what you've changed
5. Go back to the Struture Compare and right click, then select "Commit"

The last thing is that the Synchronize view comes up squished into the same pane as the tasks and console. To fix this, right click on the title of the Synchronize view and select "Fast View" to put it over in the Perspective bar on the left.