There are no file changes necessary to set up a debugger.
In Eclipse, hit the little down arrow to the right of the debug icon and go to "Debug Configurations": http://cl.ly/image/233x0R2N0J3C
. That will bring up the debug configurations window. Go down to 'Remote Java Application", right click and hit 'New': http://cl.ly/image/1a2R252U1M3P
. Most of the defaults here are fine (port 8000, localhost, etc) http://cl.ly/image/3m0F3c3f1G1W
. You'll want to make sure that you have the right project selected (by hitting the browse button) and then name it something like 'Broadleaf Site'. Then create another debug configuration but this time use port 8001 and call it 'Broadleaf Admin' and select your admin project.
Then you can hit the 'Debug' button on the bottom-right of the window to start debugging. If you have a breakpoint set in any file (Broadleaf classes or your own classes) then the little blue button will have a checkbox by it indicating that the breakpoint is set up correctly.