Hi Joshua,
Maybe I have misunderstood your question?
In any case: to manage build configurations, use the menu Project > Build Configurations > Manage.
The output folder is controlled by the build tool settings (Project > Properties > C/C++ build > Builder Settings > Build Location.
If it is about to tie Processor Expert configurations to Eclipse Build configurations: I think this is possible, but I have not used it like this.
Hope this helps,
Erich