Can "General relation features" be used in Multisite

In looking through PhpAdmin I found some ‘old friends.’ Specifically the ability to record relations — links via keys — between tables, and a bunch of other neat stuff. There are a set of procedures that setup the needed tables. I suspect that changing the database engine from MyISAM to InnoDB would drive WP nuts even though that is what I would like to do. I have a multisite setup just to keep various aspects of the application separated. I would very much like to set this stuff up; and I hate pain. Does anybody have experience, or educated guesses, on this topic?

Chris