You're never going to avoid all of the conflicts. Dodge the big ones if you can. Otherwise you just have to deal with it. Plan your music and your drill accordingly.

My JV football kids always miss Thursday. Volleyball girls always miss Tuesday. Mondays are National Honor Society (most of the officers are band kids).

I don't know why the junior high activities are causing you conflicts, unless you are in such a tiny school that you have 7th and 8th grade marching.

I make it very clear to the kids that they have to catch themselves up. I support them doing multiple activities, but I'm not reteaching what I went over while they were gone. If everyone around them knows the drill, they can usually pick it up pretty quickly. We can't do any outside rehearsal during the school day so we learn music in class. They don't perform until I am confident they know their stuff.