Welcome aboard!
The "black sky" problem may be from not rolling back Commander before enabling your mods into the game.
There is an "auto rollback" option in Commander which I recommend that you select by checking the box next to it, that will make Commander undo any changes it makes to the game as soon as you exit a gaming section.
If you do not let Commander roll back its changes automatically, then you need to do a manual rollback after exiting the game but before you enable any mods. Otherwise you are likely to run into problems.
For now, I suggest you disable the last mod you enabled before encountering the current issue. Then open Commander and perform a manual rollback. (And then select the auto rollback option if you so desire.)
Then re-enable your mod and see if that solves the problem.
Also, it is recommended that you only enable/disable mods while you are in base in between patrols and/or missions, and not while you are still playing saves made while at sea. So I would suggest that if you are in the middle of a patrol/mission right now, either wait to do what I suggested above until you have returned to base, or else go ahead and do it and chuck the current patrol/mission and start over with a new career or mission objective.
