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Met with a partner of a large firm yesterday for an informational meeting. Would it be bad etiquette to follow up with a thank you email today and perhaps mention that I had submitted an application and ask if they could give the recruiter a heads up perhaps?

Follow up thank-you e-mail = good etiquette

Ask if they can give the recruiter a heads up = assuming you do not have a close relationship, not good etiquette

The understanding is that if they liked you, they'll either already mention it to a recruiter or have asked for your resume which they would then pass on. Asking explicitly for them to let the recruiters know is a little presumptive and pushy. They know what to do if they like you. You can maybe just subtly drop a hint that you've already applied when you send a thank you e-mail, but I would leave it at that.