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.