it's funny, we're building this set up (https://github.com/PRNicovich/NicoLase) in our lab for microscopy. From the docs:

"When aligning your laser launch, do not rush. This is not something to attempt late on a Friday afternoon in a free hour before heading to the pub. This is a task involving a great amount of precision and small, careful movements. There will be very little in the way of positive results until the task is nearly complete. Set aside up to a several hours to complete the alignment, especially on your first try"

You only have to do the alignment once, on the input to the combiner cube. Then you get a single output beam sent to the galvo.