So we ended up working it out so my roommate would still do direct deposit and I'd pay the complex with checks. It turned out that while the person I talked to before doesn't like taking checks, the other office person doesn't mind.
So my roommate goes to the website and changes it so the amount they are talking out of her account is half the rent rather than the full rent she'd been paying when she'd lived here on her own last year. And we thought everything was set.
I put my check in the office on the 1st, and they cash it on the 2nd. We thought everything was fine. Only, on the 3rd they try to take the full amount out of my roommate's bank account. And since she wasn't expecting to pay that much, she didn't have that much in her bank account. So it doesn't go through. And then they try again.
So now her account has been overdrawn twice. And they sent us an email saying they will no longer accept direct withdrawals or personal checks from us (even though my check went through fine). They are saying we now have to pay with bank checks or money orders. I emailed them back explaining what happened, but they replied saying that they still won't accept checks or direct withdrawals.