Arena and tower or trials are very different from each other. In tower of trials, you grab your three or four strongest girls, pick matchups to give you elemental or class advantages when possible or at least avoid disadvantages when not, and then pop your ultimate skill when necessary to kill someone--which should be rarely on the first couple of floors but could be most battles by the end. It doesn't really matter which girls are your strongest for tower of trials other than that they're different elements and different classes. Unless you pick Trisha, who is terrible.

In arena, on the other hand, the battles end quickly, so you should generally assume that no one will get to use any skills. You also don't get to manually control your girls there. The goal is to line up your team such that you have as many elemental or class advantages as possible, so that you have maybe a 99% chance of winning, then start the match. If you can't line them up properly, then pay 2000 coins to reroll your opponents until you can.