Krishna, you dont need to compile the entire product like other simulators. You just need to compile the protocol projects. So in your case you need to compile 802.15.4 project and RPL project.
After compilation the appropriate DLLs will be created in the DLL folder. Copy paste these DLLs into the bin folder. Take care to save a copy of the default DLLs.
Then run NetSim, it will automatically work per your changes.
Yes you definitely can debug NetSim in run time. You need MS visual studio and you can put a break point, and then step in, step through, watch variables etc.
Another very useful feature is that can also open NetSim animation window and debug and visualize simultaneously.