How do I get custody papers on file if my boyfriend and I separate?

Sorry, this really isn't up to you. Right now custody isn't an issue because you (presumably) live together or have worked out some arrangement whereby he sees his daughter and he is satisfied by that. If you separate and he files for custody, you really cannot stop him. Courts will evaluate the best interest of the child and determine who should have custody and how visitation shall be allocated.

If he files for custody, than you'll likely need a lawyer. You might also want to file for child support as long as you remain unmarried. Should you ever separate, you'll be thankful that you did as that money can benefit the child. If you stay together or get married than the money benefits the family unit.