Any team that consists of two different members from the set {Knuckles,Mighty,Espio,Charmy,Vector,Heavy,Bomb} is allowed for any level except Isolated Island (where Heavy and Bomb are disallowed) and Introduction (where only P1 Knuckles, P2 Espio may be used). Use the team you think is best for each level.
I don't recall time of day having any effect on any level, and even if it does then you can choose the time that will lead to the most favorable layout.