You should make battery box which doesn't allow batteries to move at all (and connections between them). Duct tape is good for quick fixes , not as a permanent solution.
I know that you use different batteries in your setup's (interchangeable stuff) and you charge them separately, but that only means that you have to do more brainstorming while you design the box(and you can address the rain problem , while you at it). Some of the people I know , play with the battery packs the similar way and they , basically, go with slightly larger box or two smaller ones , which can accommodate batteries that they have in mind (some put theirs controllers there too). Boxes are made of fiber glass(&polyester resin- messy stuff), plywood (with some coating), or the metal (only in well-equipped workshops, with know-how). Some of them just bought plastic boxes from home depot and adapt them to meet the purpose(means - they just drilled a few holes and added some straps).