How do I ensure I get my security deposit back for my apartment?

try the sf tenants' union

take lots of pics, documenting the existing damage, then draw up something of a contract where both you and the landlord sign it in front of a licensed notary acknowledging the existence of the damage.

just one thing to consider here cuz i've been through something similar...do you think you and your roomie will leave at the same time, or would you likely leave at some point, filling the room as a sublet, similar to how you're moving in... I say this because in that case, I would say just drop it, take some photos for your own reference, but dont make a contract. that way when you move out, the new renter pays you your deposit, its no biggie, and you dont need to get the landlord involved.