You say too much overlap, then mention a problem that itself covers many areas. It's not the fact that the websites overlap that causes you an issue, and in fact this helps you because your problem might be suitable on several sites.
The problem of a given question being relevant on many sites is not a new one at all, and it's one I've written about many times.
Unfortunately, you propose two problems (sites overlap, and some questions belong on multiple sites) but you don't offer any suggestions. About the best we can offer is that you pick a site that you feel is best for your problem, or a site you feel fits your field best, and submit your questions there. The experts in the community you choose will help move the question to the right arena if needed.
But the important thing to remember about why these sites are successful is that they attract and keep experts. If we start allowing off-topic questions on a regular basis without moving them, the experts will eventually leave due to a poor signal to noise ratio.
So while balkanization seems to be a bad aspect of these sites, it's necessary to cultivate the community of experts that make these sites so useful. The overlap actually helps tie the communities together.