Welcome to the Slope!
The Festool system can be a bit intimidating, and Festool is one of the worst companies I've ever run into with regards to documenting their tools and how they are to be used. Tiny pictures in the catalog or website, unclear documentation (when there's any at all). No wonder a newb is confused.
My suggestion is to get thee to a store where people who know them sell them and ask for some demos. Go to a wood working show and hang out at the Festool booth.
John Lucas and Jerry Work both have excellent tutorials, although Jerry's tend to me a bituse larger pictures more advanced than John's. I just wish John would post larger picture links so I can see exactly everything that's going on.
[I will say that while it's possible to use the MFT as a replacement for a table saw it will be a heck of a lot more work and some stuff you just can't do (tenons, dados, coves, grooves). The parallel guides look like an importatnt improvement to the MFT/TS lash-up and get it somewhat closer to the goal of duplicating a TS but it's still not there.]
Me personally, I don't use the fence on my MFT (old style). The new MFT/3 looks like it solves the problems the old MFT had with the fence. I have a piece of Baltic Birch plywood about 1 sq foot that has 90 degree corners that have beede rail right n carefully checked. I use this to square the fence and guiderail to each other. Most of the time I use the MFT as a clamping, sanding, routing, etc station. When I want to cut with the TS-55 I measure and mark, lay the guide rail right on the mark, and cut away. Watch that the vac hose doesn't snag the guiderail and move it while you're cutting.
Use foam or an old door as a cutting station (lay them on the floor or sawhorses). WAtch your depth of cut--unfortunately the TS-55 depth stop doesn't take into consideration the 5 or 6mm thickness of the guiderail.