Which antagonist do I focus on?

At the start, the big-bad is set up to be this rogue species on the outskirts of the galaxy, who are painted as evil. Turns out they're not that evil, my protagonist ends up siding with them, and the people thought to be good guys at the start are actually the bad guys come the end. So, what exactly do I focus on? Do I prep with both of them as antagonists, but flesh out the reasons of good vs bad. Or do I prep as if I'm at the end of the novel, when we figure out who is actually good, and who's actually bad?