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I know that the second episode of AG, "A Ruin With A View!", also had members of one of those teams. I can't remember which one, but they were there. There was also "Stairway to Devon!" that had Team Aqua.
Other than those two episodes, I can't remember what other episodes they were in.
Going chronologically and covering all the A/M episodes.
Advanced:
Magma-only:
A Ruin With a View
Aqua-only:
Stairway to Devon
On a Wingull and a Prayer
Both:
A Three Team Scheme
Magma-only:
The Spheal of Approval
Advanced Challenge:
Both:
Fight for the Meteorite
Aqua-only (99.9% of it, anyway):
Unfair-Weather Friends
Advanced Battle:
Both:
Gaining Groudon
The Scuffle of Legends
Mentioned in passing:
The Ribbon Cup Caper (featuring an ex-Magma agent)
The Scheme Team
That should answer everything for you. I'll leave it open for the night, in case there are any other episodes that verbally references them. Not counting anything on PUSA, but I'm pretty sure they didn't...yet.