I'm doing basketball leagues as well, how I would handle your situation is this:
1). Set up three leagues, one for each age group.
2). Set each league to 'championship' in the league preferences.
3). Set up four groups in each league, one for each region, also in preferences.
4). Set the 'Teams to advance' to 1, so that the winner of each group moves on the the finals.
The only problem you might run into is that, unless I've missed something somewhere, you can't set up games outside a group in Championship mode, I had to write some code for that. I've seen 'Inter Group Matches' in a couple of places in the code, which seems like it might be what I'd want, but I'm don't see any way of getting it to work so I fixed it myself. If you only allow games within the group, 'championship' is perfect, if you need the other code, I'll clean it up and make it available.
So far, this set up is working well for me with the leagues I'm working with that will have advancement out of a group, the prelim games are still being played, and I haven't had time to tackle those tests yet, I probably will next week.