I’ve searched for an answer for this but can’t find it!It's not uncommon, and yes, you can submit the work your agent isn't interested in on your own.
What happens when you query an agent, they ask to see several things at once, and like one or two mss but not the rest? I am a published author but have a few pb mss and a new MG ms. Agent is very interested in the novel but not the picture books. If I sign with the agent, does that mean that I continue submitting all the other “stuff” on my own that the agent doesn’t care for while agent submits the novel? Is that a common thing to happen where an agent only submits some of the authors work (the mss they like)?
Just don't reference your agent in the query/original submission.
(a) Generally, if you have an agent, your agent is submitting for you, and that's what editors expect.
(b) Mentioning your agent makes it sound like maybe you expect the submission to be treated as an agented submission, but if your agent's not behind it, then it hasn't been through the filter that awards it special consideration at publishers.
(c) Editors are also sensitive to the possibility of author scams (see post below 'cunning stupidity'), so a submission from someone who has an agent but whose "agent" isn't sending the submission raises a red flag.
But talk to the agent in question about this: there are lots of different styles of agenting, and you won't know which one this agent has until you ask her.