The process is identical for both, actually. just means you dont need anyone else to update.
Yes, the version number appears on the zip file, and is the easiest way to tell the difference. eg. "MFR_1.0.5b"
I added the zip file to the mods folder, took out the old one and launched FTB, but when i tried to open my world, it said there were ID mismatches and it said that the MFR blocks were missing. How do i fix this?