The sites overlap a lot. U&L is largely a subset of Super User, and Ask Ubuntu is largely a subset of both. That said, there are some areas which aren't contained in the more broad site, such as Super User probably doesn't want all our shell scripting questions. And we probably don't want questions about Ubuntu the organization. And of course there are lots of topics that Super User is OK with that we don't want, such as Windows.
Note that there are overlaps with other sites too; for example, we overlap with Stack Overflow on scripts & the Unix API.
How, then, to decide which site to ask on? Let's assume it's something you could ask on any of the three sites, as if it only fits on one, the answer is obvious.
If you want an answer that may use Ubuntu-specific things, and will probably be focused on doing it through some GUI if possible, ask on Ask Ubuntu.
If you want an answer that'll assume familiarity with the command line and basic Unix knowledge, or that will work on multiple distros, ask here.
I wouldn't suggest asking on Super User ⃰ unless there is a substantial overlap with one of the other OS's they're more familiar with. E.g., you're trying to get your Linux server to talk to your Windows client, and you're not sure which side is misconfigured and/or broken.
* If you asked me on chat, I'd say to ask there if you want a wrong and/or misguided answer, but that's not really fair to them—they've got quite a bit of Windows expertise there, we have Unix expertise here. We'd probably give you wrong and/or misguided Windows advice.