It's not necessary for your agents to specialise - they could join a Freelance division of their preferred department, working across multiple fandoms. (Most agents do, these days.) They could also join the Department of Floaters, which doesn't specialise in anything (though that does mean you should make an effort not to turn everything into a Mary-Sue hunt).

It's not necessary for you to know everything about a canon before you write missions there - no-one does! Even Jay and Acacia made mistakes occasionally (they claim once that Legolas left Middle-earth immediately after LotR ended, for instance), and there are such things as reference materials. Heck, I've written a mission about a movie I'm not sure I've even seen, just by asking people who knew it and glancing at a scene on YouTube.

It's also not necessary for your agents to know everything. The 'agent is sent into canon they know nothing about' plot is established enough to qualify a trope - and again, there's reference material available. It can even make it more interesting - send your agent in with a printout of the relevant fan-wiki, and see what it does to the plot! (They could drop it, complain about how incomplete it is, find it's been edited to be flat-out wrong... let the imagination run wild.)

So there you go; three answers to two questions. ^_~

hS