As of a several years ago now we are allowed to use multiple main/primary tags. Just got to adhere to the areas limits for number of deer tagged per person (1,2,5) and make sure to have a buck tag for a buck, and a doe tag for a doe. So it is perfectly legal to use a main rifle tag on a doe in a lottery area after winning the lottery, then to use the main muzzleloader tag on a doe or buck in a managed area during muzzy season. Heck, could even go buy a bonus tag and get another doe in the managed area as the 1 lottery deer doesn't count against the 2 managed limit.
Page 69 or so of the regs.