This topic got to 1000 views while I wasn't looking! Thank you all for reading my posts. We're going slowly but steadily right now, progress is still being made!
So lately I've been allocating levels to the overworld. These two things are designed mostly separately, as in that the overworld and level design do not influence each other in a major way. We produce a bank of levels, a bunch of overworld rooms, and then start to allocate the levels to those overworlds.
This was a bit of a vague process, but since of late I've been able to get a bit more structure into this: by simply sorting all levels we created on difficulty, giving it a number between one and five. Then I look how the general difficulty distribution is, and if it's all right, I bundle levels of similar difficulty levels in groups. If there are not enough levels to fill an entire group, that means levels need to be adjusted or new ones need to be made to fill up the gaps. Such a group can then be distributed across one spaceship in the overworld. The list also keeps track of levels that might be more frustrating than have fair difficulty that need to be polished.
This might seem like level design 101 for some, but who hasn't hit an annoying difficulty spike in some game which took eternities to overcome, if at all? I mean, my game does already do a lot to combat that (by offering difficulty selection and other options), this is just another step to a game that builds up the difficulty nicely, and just good game design overall.
I'll have more screenshots for next time!