SKSE injects more things into the game for modders to use. Commands in the console for them to play with and make scripts more efficient. Dragon Script runs scripts from outside the game that can be written in C+ I think. They both do great jobs of adding more options for modders to use in game. They shouldn't conflict at all as they are run entirely differently. As for fps hit, it may be the mod that required you to install SKSE, it shouldn't affect the game really at all. It simply adds more commands.