You need to have the box in neutral when you put it back together Russ but that's easy to do, you can take the cover off without it being in neutral.
You need to stop the kick start lever from spinning forward when you take off the cover, do this by using the clutch lever to stop it turning forward ( turn clutch lever outward from the box while holding the kick start lever back, then let the kick start lever come forward and rest upon the clutch lever as you remove the cover.
Do you have a manual of any type?
Ask again if you need to