In this folder:
https://github.com/EQEmu/Server/tree.../utils/patches
The patch_RoF2.conf file from your source in utils/patches/ needs to be copied into your server folder where you should have copied the other .conf files. That is all you should have to do.
Make sure you are compiling the latest source yourself if you want RoF2. There are no pre-built windows binaries available for RoF2 client yet that I am aware of.