Welcome to SUBSIM.
One of the mod I can suggest you is H.sie's Hardcoded Fixes if you haven't tried that. One of the mod's option is send automatically your Watch Officer back to the conning tower after your uboot surfaces.
If you are tired to manage your crew, I can suggest you to use SH3 Commander to set the fatigue either to "no fatigue" or there are a couple of different fatigue models. There is a post in this forum whatever is a job for the Captain to manage each crew one by one or not. Both sides have strong arguments. For me, I go with GWX 8 Hours Fatigue Model, It adds dimension to the game.
When I need to manage my officer I generally do this.
In case of no danger, I only man the Chief Officer and The Watch Officer. The other 2 officer are resting. One in the Stern Quarters and One in the Bow Quarters. When the officers on duty became to get tired I replace the one in the stern quarters with the Chief Officer and the one in the Bow Quarters with the Watch Officer. If you have more than 4 officers, and you don't have the space to rest them, try sending them to the compartments where they won't get tired compared to the other departments.
Repair and Torpedo Rooms (even if there are no repair or torpedo loading/unloading) are the most tiring compartments if I don't remember wrong. The less tiring ones are Electric and Diesel Engine compartment I believe.