Do I need to separate the male and female rabbits after she gives birth?
I did not know she was pregnant and she had 8 and 1 passed. I thought I had two boys until I saw her nesting today and then a few hours later there were babies. I tried to move them because she had them in the litter box but then I moved them back so I did not upset her. Please help I don't know anything about this stuff.
Yes! Move the boy out, or he might rebreed the girl right away. (It is probably already too late.)
I think your first instincts were correct - to move the kits out of the litter box. The mum knows you - she'll be okay. Just move the kits with the fur and straw and other nesting materials to the girl's 'bedroom' or clean area of the hutch. Don' be afraid - the doe only feeds the babies once a day, so if she seems to be 'ignoring' them, everything is still fine. Check the kits the next day - they should have nice round tummies by then.
Either of these two resources provides complete information on how to deal with surprise pregnancies and litters:Rabbit Raising Problem Solver Rabbit Reproduction E-Book
Good luck, and have fun!