Yeah as other have said, Whale Ship is basically as follows:

Order by Total Atk 1st, Shuffle top 2-3 teams around till the 1st team is all or as close to all the same colour as the runs you will be doing, go to last few teams and replace girls with the mission colour till ship changes colour (16 girls total of that colour needed). And that is it.

You should never to almost never lose girls on the deck and your ship should never die. If either of these things happen a lot then you are probably not strong enough for this yet.