Hi Tommy! Welcome to Ninjette !!!
Yes, flat where it meets cylinder-head. Grooved on cover side.
Don't use silicone, it doesn't stick very well when there's oil around. Also on newer bikes with EFI, it tends to sneak through to exhaust and foul up O2-sensors. Use FIPG material such as Toyota 00295-00103, Yamabond-4 (not 5), Permatex The Right Stuff Grey.
Apply where manual instructs. If you want, apply just tiny bit on flat side, a fishing-line sized bead. Top side not needed due to groove and labyrinth sealing. Also don't over-tighten valve-cover bolts. They bottom and stops pressing on gasket after certain point. More torque will just snap valve-cover bolts.