"누구 편을 들어야될지 모른다?" ; You can use this sentence both good and bad situations.
"누구를 응원을 해야될지 모른다"? We usually use "응원" to sports like soccor, baseball, and race.
응원 is bright meaning like cheers.
BUT......somehow 편 is negative meaning like partial opinions.
For example, two friends are fighting now. you can't say "응원" here. (If you do, you will get in trouble.
Saying is that you rise a quarrel more.)
You can say "편" --> "나는 너 편이야.";I'm on your side. It sounds like dividing into 2 sides. not nice, I guess.
Another situation is that you go to watch a soccer game.
Someone will ask you "누구 응원하고 있어요?" or "누구 편이예요?"
Both are OK but I prefer "누구 응원하고 있어요?" here. softer and milder. *^^*
I'm not sure whether you understand this well or not.
If not, I will get another example for you. let me know lol