The attacker decides whether to retreat/submerge before the defender decides whether to submerge, so your friend could retreat before you could submerge.
Each airbase can only scramble 3 fighters. If you have more than one sea zone serviced by that airbase, you have to choose from the 3 planes which ones go to which sea zone. Yes, you can split them up if you want to (2 to SZ 109, 1 to SZ 110, etc.).