Thank you to the Twitterverse for this great question.
Is it okay to query agents with different manuscripts, or should an author focus on one at a time?
My blanket answer is that you should only query one manuscript at a time. However, I know many authors dabble in different genres and might be querying completely different agents. For example, if you’re writing both middle grade and adult thrillers you might find agents at the same agency to query, but it might be more difficult to find one agent who represents both genres. In this case, I would suggest you feel free to go ahead and query both manuscripts at the same time. However, when you do find an agent you might be forced to put querying of the other manuscript aside, at least momentarily, while you settle into building a career with that first book.
If however, you are writing in one genre I would suggest you stick to querying the strongest, and presumably, the newest book. I’m not sure it benefits you to be inundating the same agents with multiple books. They are likely to judge you on the first one they read anyway and, again, presumably the newest book is your strongest book in which case put the first one aside and query with the material that’s most likely to grab you an agent.
Good luck and happy querying!