I'm one of the few people I know who loves portable churches.
1. Good cases are not an option. LM Cases, Road Ready, PCI, etc. They all make good cases that hold up well, as far as I've seen. I've been in portable churches where they try the cheap, somewhat flimsy cases to store things and they always crush at some point and something gets broken. That gets expensive and you don't want to find broken equipment at 7 o'clock Sunday morning. If your budget is real tight, I've also used some Stanley cases. They have large wheel and pull-out handles. They hold up pretty well, too, but I wouldn't put a mixer in one. =) If you fight for nothing else come budget time, fight for this.
2. Figure out where everything is going to go and get it labelled. On each box/case, put a digram of the room it goes in and where it should be placed. That way, even somebody who's showing up to help the first time can get it to the right place the first time without needing to stop somebody else.
3. Also, organize the boxes and label them. The same equipment goes into the same box the same way every week. You don't want to be hunting for cables and connectors when you're already limited on time.
4. FOH cases hold FOH equipment. Stage boxes hold stage equipment. When they mix, even if labelled properly, your setup takes longer as people walk back and forth for things.
5. Wheels. Everything should either have wheels built in or available. That could mean dollies and furniture carts. Whichever it is, protect your workers' backs.
6. Label. Label. Label. Cables should be marked in some way to show length. Some people use color coding; some use masking tape and the number. Whatever works for you. Input sheets should be provided each week for stage snakes and mixers. The more people can do without consulting the "tech guy" the more efficient your setup will be and the easier it'll be to plug in new people.
I may think of more, but those are definitely the big ones for me.