Hi - I sand the whole thing. The idea is to start with low grit sandpaper and cut the layers. It will be difficult (imo) to sand one area only and have it unaffected by the side to side action that will go over to other areas.
Depending on the severity of the marquee (plexi) scratches, deep scratches that my fingernail can get into, i may start lower on the grain scale. 220 typically. The reason is i am tearing down the plexi to lower level and once i get there, higher grit paper will get rid of the micro scratches i caused.
For lighter surface, i start with 400. When you are done with 400 or 220 (sanding from side to side), you will panic - the thing looks worse than when you started.
Dont worry - go to 600 grit, 800, 1000, 1500, 2000. At each point, clean up the plexi and see the improvement - the surface scratches are getting buffed out by the increase in grit.
For application, I do combination of Wet (wet the paper with spit or spray cleaner), dry, and, YES, NOVUS. Novus 3 followed by novus 2, using that near the 1000 - 2000 range.
This does the trick. In the last week, ive got a dig dug marquee looking nice, Tmolding looking almost new, and the back of my truck has plastic that was all deep scratched and sanded that out too.
Sanding rules!