It is generally accepted that you should only query one, and will usually state as much in the submission guidelines for any given agency. In most agencies, the agents talk and will pass around your submission if they think it's better suited for another agent. I've even been asked by an agent if she could pass my full along to someone else in the agency. If there's an agency where you're especially inclined to simultaneously submit to multiple agents, I would strongly suggest first checking their submission guidelines to make sure there's no blatant rule against this. (But honestly, with simultaneous submissions, I just wouldn't.) Same goes for querying another at a later date--in some agencies, this is OK. (I forget which agency it is but I know there's at least one that specifically states "If X says no, you are permitted to then query Y," and I'm pretty sure they both rep contemporary YA.) In some, a no from one is a no from all. The best way to know which are OK is to look at their guidelines and look them up here as well for extra info.
As for knowing which agent to submit to when several represent your genre, try searching online for interviews or wishlists, or following them on Twitter to see what specifically they're looking for. You can also look at what books they already represent. You may see that for one, they really like dark, edgy contemporary YA while another wants beach reads. Or one likes "issue" books while another likes romance, etc.