(Not 100% sure what you mean by "effects box groupings". I think I'm reading this correctly. Seems too simple a solution, maybe I do have it wrong!)
Set up a series of patches with whatever effects you want in them and hit the three silver switches to turn them all off as you set each up.
Move on to your next patch and do the same thing.
The B3 will remember that all the effects were turned off when you used it last and next time you call those patches up the effects will be already switched off.
Is that what you want?
'80 Rick 4001. '84 Fender Power J Special, '05 USA Jazz, '11 USA Precision, M Miller Jazz. Peavey T-40, Zoom B3. GB ShuttleMax 12.0, GB Uber410, fEARful 212.