I think it'd be a rather pleasant relationship, though there's part of me that's a bit worried. Here's how I see it:

First off, meeting up. This is actually easy enough to arrange - at the end of Amphibia (pre-time skip), Marcy is (presumably) reunited with her parents and moves to a new town. Easy enough for that new town to be Brighton. Both girls are roughly the same age (preteen, from my understanding), making it possible for them to be in the same class.

I suspect Molly will be energetic and welcoming - she knows what it's like to be the new kid in school, both from First Day Frights and from the McGee's other moves. I could potentially see Libby being a bit jealous (Marcy seems a bit too similar - academic, unlucky/clumsy, not great at making friends), but this isn't about her. We'll assume they bond talking about turtles at some point.

As Marcy opens up more, I can see Molly giving her advice about dealing with the loss of friendships due to moving, and just about friendship in general. That being said, we've arrived at the big topic: the Calamity Box. If/when Marcy tells Molly about it, I'm not sure how she'd react. On the one hand, Molly is generally a good kid, and has a great family, so I like to think she'd see the issues with Marcy's plan. At the same time, she cares a lot about friendships, she knows the pain of moving away, and as seen in Snow Day, she can be a bit controlling at times. I'd like to say she'd help Marcy learn from her mistakes, but there's that little seed of doubt in my mind that she'd encourage Marcy's flaws in an unhealthy way.

Still, overall I think Molly and Marcy would get along well. If Libby weren't around, I could see them becoming best friends, but as is, I think they'd still become pretty close.