Generaly you can select casualties for your opponent (take infantry before artillery, artillery before tanks …)
If there is a question (attacking sub gets 1 hit on a defending transport and a sub), then save the game when it is your opponents turn to select casualties, exit the game, and mail the saved game file to your opponent (this works better in 0.8.2 than earlier versions). Your opponent can open the saved game, select casualties, and continue the battle.