Do I need to transfer the ships out there? I know I can transfer modules to Colonia and back to the bubble but seems like I can't mod any unless they are in a ship at the time. What the most painless way ? Have 4 ships to mod
You need to put the modules in a ship - but you can probably buy a ship to hold the modules out here [1], so you can just move the modules. On the other hand, if you're not short on money, it'll be easier to just move the ships.
Alternatively, if you want the engineered modules to be in the bubble, just pin the blueprints and fly back to the bubble, then modify the modules there with the remote workshop and get a bubble engineer to add experimentals if applicable. (There's a bug where pinned blueprints unpin themselves, so after pinning them all, quit the game, log back in, and if they're all still pinned you're probably good to go)
[1] Exception: the Cutter is currently the only ship that holds that size of Thrusters, Sensor or Life Support, and you can't buy one out here, so you'll have to move the ship too.