If I get you correctly, you are just clicking sync and then looking in your IDE.
I successfully used Mododev for debugging in Unity in the past, but it was quite a while ago, and I'm afraid I cannot remember much. However, I do know that "Syncing" actually just creates an SLN file which needs to be opened by MonoDevlop. I believe that is created somewhere in the project folder. After you open the sln file in *Unity's* MonoDevelop build, you should be able to run the program. Doing this will open a second copy of Unity. From this second copy, you can run your program.
I believe that in the monodevelop IDE you can edit the source files you created and place functional breakpoints that occur during Unity runtime if that makes sense.
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