2nd affection makes a huge difference. I ran a map shortly after it was added and I had 2 squads that use to have equal damage output. I gave second affection to all of the units in the squad and while the one without 2nd affection did fine the squad that got the boost absolutely eviscerated everything in their path.

You also get 2 flower gems for hitting 100% 2nd affection, so there's that as a bonus as well.

Also, about the Whale Ship missions:
Equip as many girls in the squad as possible with equipment items. Those can actually decide between a success and a loss here.
You also want to choose the strongest (in TP) helper you have for the more difficult missions.

Generally, you'll have your strongest girls in your regular squads anyway, so I'd suggest making the first four squads (20 girls) of your Whale team the same as your regular team. Maybe adjust the order of the squads, to make sure the absolute strongest squad is leading, but that's it.

The fifth squad is a good place to put some girls who support your entire whale team. Especially girls who give you a start with how far your Light Gauge (for the Solar Blast) is filled work well here, but also girls like Chocolate Cosmos and Strawberry Candle for their bonus nodes. Unless you have those girls in your first four squads ofcourse, no point moving them away from there.

The sixth, seventh and eight squads can then be used for "colormatching" the boss. If the whale boss you're fighting is weak to hit, then fill up these last squads with hit-girls. If it's weak to pierce, fill these squads up with the best pierce girls you didn't use yet. Colormatching the bosses' weakness increases the damage your whaleship deals (like fighting regular pests), and effectively allows whaleship team to handle bosses that are 30 to 50 percent in suggested difficulty above your ships' powerlevel.
Do note, the latest boss that was added is colorless (grey circle, no icon), and to get a bonus against it, your whaleship too has to be "colorless", i.e. have an even distribution in girl-types.

One piece of advise the colour matched teams it's best to have your strongest 5 of each in team one as all the deck enemies will be weak vs that class, not a huge thing but helps the fights go quicker

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.

I really think people who cannot clear W1-5 should not do whaleship. At least W1-4. Anything below that is too inefficient imo.
You might get more out of running missions to make yourself stronger.

...that's a fair point, if you're struggling to do that and slipping on behind on other things that's probably a waste

Thank you for all the help provided, guys.

Looks like I did better on the whale now since I could clear the first two stages of Mission 1 (Well, my strongest girls are slice after all), but since the next one requires a 800,000 power level and I'm only at 750,000 I think I should focus on leveling the dozens of underleveled girls I have.

On that topic, I usually tend to neglect most event girls and leave them with no equipment. From what you guys said, equipment seems to be very important on whaleship. Should I fully equip all my girls or only bother with that if it is the special equips? (I don't have that many). I didn't even bought the dressbloom and skillbloom of the new girl and went straight for the equipment and atk amps. Guess I should correct that, right?
Also, If equipment is so important now should I prioritize those upgrade material before lvl100 manyu and amps?

And sorry for the noob question, but what mission is W1-5?