After adding indium along with connected glass mods, it doesn't give me any option to toggle connected glass or any of the other options

Do you only see this with Indium and Sodium? It sounds like you've misunderstood what Connected Glass does. It adds new types of glass. It does not modify existing glass like Continuity, Athena and Fusion do.

For reference, I'm using Connectedglass-1.1.11-fabric-mc1.20.1.jar sodium-fabric-mc1.20.1-0.5.3.jar and indium-1.0.27+mc1.20.1.jar

This doesn't sound like an issue with Indium, please report the issue to the authors of the connected glass mods you're using (or maybe you've misunderstood what the mods do?)