For your first question, unfortunately, that was not something that I had thought of when I originally wrote the program. It will probably pick the first one it would find in the database, which normally* would be the lowest number. (*It might be a higher numbered ship if a lower numbered ship was destroyed, hence deleted from the database, and a higher numbered ship was created later filling the lower number's place. Of course, you'd never know when that might happen because it could even be in a different game. Sorry about the db mumbo-jumbo. I just felt like that needed more of an explanation than simply saying what normally would happen.) I can probably modify the system with a drop down menu to select which ship your guys are loading onto.
Regarding your second question, at this point, the entire system works with only the present status being recorded. In the Battle Log you can see the history of what has gone on, but that is only a textual description and there is no way to back up what has gone on even from that because there are so many other elements that are not recorded. I have wanted to have a playback feature so that people could replay what was going on during other players' turns, but that would require a major rewrite of the system to accommodate it. It is something that I would like to do eventually, but not something that will get done soon at all. A shopping cart system using temporary storage for the purchase phase would be much more feasible as a short term goal.
By the way, I have been making progress on the next update to the battle system. I'm not sure if I'll be putting it in as an option to the system or a solid switch. The current battle system plays through one round of combat. If all the defenders are killed, the attackers win, otherwise any surviving attackers retreat. The new battle system will be a fight to the death.