This isn’t as complicated as it might seem. Simply explain the situation and let the agents decide. Contact the agent you were referred to and say that So-and-So referred you because he thought you’d be a good match . . . you respect So-and-So’s judgment but must point out that the manuscript is already with Colleague Agent . . . you respect the entire agency and would be honored to be represented by either agent . . . you’ll respect the agency’s decision about which agent should handle the submission. That’s respectful (three times over!), forthright, and appropriate. I was in a similar scenario as an editor, and all it took was a quick phone call, one editor to another, to decide who’d handle the submission. Easy-peasy.
What a glorious position to be in. 2 agent referrals. That’s the way I look at it. And I agree with Dear-Editor, being honest and “respectful” is always key. Not just for agents, but business in general. I get situations like this in my day job all the time. What wins the day for me is when someone is polite and honest. Then they’ve earned my “respect” as I imagine you will the agents’. Good luck!