Could you be a bit more specific? What is the purpose of the -Xmx and -Xms arguments? Are you trying to compile?
In your source list on the left, there's a Group titled "Executables." (If I understand your question correctly.) Expand this group, and click on the executable you want to add the options for. Click the "Info" button in the toolbar, then on the "Arguments" tab of the window that pops up.
This is, as far as I know, the easiest way to add runtime arguments to the java compiler from within XCode.
I set the heap size all the time in Xcode and it works fine. Just do what Littleodie914 says. Add an argument for the executable, and make sure it is ticked. Just put in what the argument is, eg -Xms256m -Xmx256m. Don't use name= value= .