You can only run two trains with this layout without fear of them crashing. I'd look at a way to adjust it so you can run at least three trains, otherwise it does look like it'd be fun with the trains crossing allover.
As for FasTrack on the floor, I'd say do it. My kids love when I do. Be sure to get a few of the grade crossings that don't have signals for them to drive their cars across. They love driving their Hot Wheels and LEGO cars across it, building Duplo tunnels and LEGO buildings. I also use empty gondolas and hoppers as "passenger" cars so they can put the LEGO mini-figs and other figures and small plushies in them.
