FSO is the engine. Media VP Upgrade is the new models for that engine (which can also just use the stock models).
For normal FreeSpace 2 with the new models you want to load the Media VP Upgrade yeah.
If you want to play upgraded FreeSpace 1 that's called the FreeSpace Port (porting FreeSpace 1 missions + upgrades to FSO).
Many times a mod will require another mod to function (example, it requires Media VP Upgrade). If this happens you just select the mod you want and it will chainload the required mod (MVP Upgrade) automatically for you.
The old installer still had you selecting the mod to play from a drop-down (would me listed as Media VPs 3.x or whatever IIRC). It's just a new skin over the top, the SCP engine is still executing -mod MediaVPs3.x or whatever in the background, if I understand correctly.
EDIT: Oh, didn't see the next page there, I see wookieejedi responded already. If KNet is the new thing I'd probably try that, looks to be a revamp of Knossos so see what you get there.