You can do both really. If you're happy enough with the mix you've got, you can bounce down pre-eq'd stems, but you have to bear in mind that with subtractive EQ you are cutting away information that you can't put back in. So if you later think something doesn't sound quite as full as you like, its better to cut less away than try a boost a stem thats already had stuff cut away.

But again, depends on your groups. I tend to leave EQ on, bounce down into groups then EQ the groups a bit more for tweakage, and maybe add a touch of delay and subtle verbs for added depth.