1) If I query an agent with 3 manuscripts and she doesn't accept any, but then likes the 4th, does that mean she's not interested in representing the first 3? 2) If I have one agent that likes manuscript A and another agent that likes manuscript B, what's the best agent choice for me?
Okay, so we've established that you're prolific, and you're clearly improving because you've gotten interest. Congratulations! This is important, and remember that once you're in the situation to ask Question #1, let alone Question #2, you're in a place of choosing between good and good, as opposed to good and bad, or no choices at all. Therefore your first job is to take a deep breath.
Take a deep breath and remember that you're in the communications industry.
The answer to Question One is: ask her. When she calls to talk to you about representation, after you guys are done discussing the current title, say, "I don't know if you remember that I'd previously queried you, but I happen to have other books I'd shelved. Would you be interested in representing those as well at some point in the future?"
But before you go ahead and do that (I'm assuming you're not on the phone right this very minute, so I can go all out of order here) I want you to consider that at this moment in time, is it possible that you yourself don't want those books out there?
Because you've grown as a writer between Book #1 and Book #4. Is it possible, just a little, eensie-weensie bit possible, that Book #1 got rejected because it isn't up to the standards of your current book? And because you want only your very best work out there, maybe you aren't going to want that shown to editors?
Your agent will most likely want to submit only one book of yours at a time. She will doubtless be delighted that you have other books up your sleeve, but she may hold them back because when an editor calls and says, "We must have this author," she can then say, "You know, she's actually got another book she's working on that has me even more excited!" Can you say two-book deal? I'm sure your future agent can. Even if the agent doesn't sell both books out of the gate, the agent may dangle a second book before editors as a little extra bait: you liked this book so much, and she's already written more…you really don't want to chance another publisher snatching this up, do you?
But again…are those books your best work now? They were your best work back then, but haven't you learned and grown in the past couple of years? Go back and look at them. Read them out loud. Do you flinch often? Does an important plot point seem contrived? Do you want someone to pick that up and judge the rest of your work based on it?
On the other hand, some books are just not good "debut" titles. They're solid books, but they would do better as a writer's second book because they're a little more risky. Maybe your previous books fall into that category.
So this is my recommendation: if the agent previously requested pages off those books, then by all means talk to the agent about them. She may remember why she rejected the other books. If she only rejected based on the query, mention that you have them but don't push too hard. Ask how the agent wants to look at your unpublished backlist. Ask. Because you're both in the communications industry, and you should be able to communicate.
Question Two is in the same vein: if you have two agents offering on separate projects, then talk to each agent about the other project. Ask how they would handle the two titles. Ask how they would handle your career if the books are in two different genres. Ask if they have good contacts and have made sales in both genres. You notice the theme here, right? Talk to them.
I can't address who is the best choice for you, but you're going to be the one on the phone. You'll be the one who hears their voices, who feels like she's being sold versus feels like she's being courted. You're going to have to figure out which is the one you'd like to have lunch with, who is the one you'd rather call up when you're about to miss a deadline. You figure this out the same way you figure it out when they're both offering on the same manuscript. And if you did your research ahead of time, you don't have to worry about being scammed, so you're choosing between "good" and "good." That's a nice place to be. Breathe. Relax.
Most likely each agent will ask to read the one the other is offering on. Send it. Ask while you're still on the phone what they do with clients who have multiple manuscripts. Ask which they'd prefer to submit first. Write down everything they say, and then later, go back over your notes and try to think about which agent made you feel most comfortable, which agent's ideas about your books felt most in line with your own.
But in the meantime, keep writing, and keep growing. If you're getting this kind of interest, it sounds like you're practically there.