What should I do? As of right now I have my 3 year old daughter 64% of the time and her mother has her 36% of the time. I can't afford a lawyer. I make minimum wage which is like $8 in California. I've heard things like like legal aid but I've also heard that there is some paper work I can get through the courts where if she signs it I won't have to go through court..

No, you heard wrong. You need to do it through the courts. Most courts will help you fill out the needed paperwork and since you both agree then it is a slam dunk and the judge signs it off. You need to apply for modification of custody and have the courts approve it so its legal.

Agreed, you have to go though the court to modify your agreement, this will effect child support orders, and custody.