It wasn't so bad, I used google's spreadsheet and it allowed me to easily visualize how the skills were arranged and how I could share officers. Anyway, I've tested out the new arrangement for the Promethus and its a pretty good setup except for one flaw. As I am heavily using Tactical Team and Science Team, I quickly realized Engineering Team was never ready when I needed it most as these three skills share the same cooldown timer. So I think I need to replace Engineering Team with another hull repair skill.
Can I apply two Hazard Emitter skills at the same time?
I sometime use Excel or just draw a matrix on index cards. Without actually spending time to analyze what you posted, I think you're on the right path. (Just looking at the skill titles.)
The thought process that I use when building is:
1) What do I want to accomplish with this ship?
Sounds like common sense but you see a lot of people that can't decide what they want so their ship is half-ass.
2) What BOFF skills are needed? Again it sounds like common sense but you see people with skills like Cannon Rapid Fire and they don't have any cannons.
3) On some skills, the effects between level I and II or III are negligible so grab it at Level I and use the LCDR/CMDR skill slot for something else.
4) Don't forget that you can train your BOFFs in some of the Level III skills by using the Rare and Very Rare BOFFs.
5) I might use a temp skill at Ensign level just to survive then change out to permanent skill later. Probably a bad example because it's a ground skill but I would have a tac photon grenade I starting out. Later, I'd give him some other Ensign skill and give him photon grenade II or III.
6) Don't forget your DOFFs! Find ones that boost the skills that you're using. If you use torps a lot, find a rare or very rare Projectile Weapons Officer. Don't forget that you can mail unbound DOFFs between your characters.