I am not sure about combining leagues - do you mean take two different universes you already have and merging them together? Maybe that can be done somehow but I don't know how.
As for sub leagues, you can't "officially" have more than two sub leagues but there are ways to unofficially do it The main way these days is to use the Association function which was added in OOTP 13. This lets you create a "super-league" which has several leagues under it and gives you a lot of options in how it works. So you would create a league for each sub-league you want, add them all into the association - then use the association setup options to determine how you want playoffs, drafting, trades etc to work inside the association. You can have combined playoffs, trading, etc but there are still some limitations like separate league hall of fames, etc.
Look here for all the stuff you can do - lots of info in all the links from this page.
Out of the Park Baseball Manual