yea def get glass for baffles instead of acrylic. i made that mistake. glass baffles will seal and bond beautifully with the tank, acrylic wont. you'll have to goop the silicone everywhere just to hold the acrylic in place, but it wont bond.
home depot sells different size small glass panes... get the small cutting tool in the same section and cut them to size. but be very careful and wear gloves. i cut myself about 45 times doing mine.
and as far as size compartments it all depends on what you want to put in each. some people need a big first compartment to fit their skimmers, etc. there are many many different designs and sizes that people use.