Extending and modifying the way modules work is most of the time really easy with hooks. With good enough design most of the modules can be made to work with each other seamlessly, but sometimes gluing modules together might get a bit painful; some time ago I was presented with a task to make Facebook Connect work with Domain Access. Within the projects technical parameters the only way to go about it was to do some detective work and code the functionality.

I will now give you an example on how you'll get it done, also this will serve as an example on how to glue together two modules and possibly benefit the community :) A warning though; this is quite code intensive and some experience is needed on how Drupal works. Also it should be noted that fbconnect and domain might not be the best modules to glue together, but stuff like this should not be feared.

Note that the result was posted as an issue/patch to d.org here.