This will be a list of the various ships and the "Command Officers" mentioned above.

3 military ships (well sort of)
Centaur Class Faststar Chiron
Atlis former small passenger line. Now an exploration ship able to carry a pair of Raptors.
Herse originally a Colonial Postal Service ship now used as long distance exploration ship.

Civilian ships 23 total
Maxon Mining
Maxon's Respite is the headquarters, R&R ship, and has some light industrial capacity for some repair during standard mining maintenance needs.

Mining Ships 6
Chrysos ("flagship" of the mining division for MM. was Carl's ship)
Sidero
Iridio (was full of ore at time of attack)
Asimi
Chalkos
Ermis

Ore Ships 2
Spasimo
Syntrivi

Tyleum processing ship
Venzi

Tyleum refueler
Apovlita

Hydroponics Ships
Sitira
Ryzi

Waste processing ship
Prymni

Water processing ship
Limni

Cargo Ships 3
Epsiki (holding 3 scrap ships)
Fortio (holding former CeeMart 264)
Syron largest cargo ship (was 70% full of tyleum at time of attack)

Ships picked up since Cylon attacks

Banshee mining and Tomas Decat's ship
Quincy ore ship. Converted to tyleum processing ship.
Oliver cargo ship
Vega larger flat top repair ship Captain Lindon (former Ceemart 264 Captain)
Linnet medium cargo ship Captain Baxter (former Herse XO)

Commander list

Commander Ronda Jasper
Colonel Dominick Marton
Major Marcia Anders
Major Trevor Limaki
Captain Randy Hamlin
Captain Zoe Talbot
Captain Shayla Tonis

They are in the above order. Anders was promoted just before Limaki as she has better Command training even though Limaki had far longer as a Captain. Talbot was enlisted and served on the CIC of a previous ship. She has bridge experience and officer experience if not bridge officer experience. This is why she was put as XO under Marton so he could see how she did. She did as well as expected as a brand new XO.
Like I said above if they all died then whatever LT was senior would be the new Commander with various orders written up. Of course that everyone senior would die but anything of value surviving is unlikely but I really didn't like how "slapdash" the Command structure of the Galactica was. Plus now with I can have the three ships with a Captain and an XO. That an XO is missing that will come up in the next chapter.