www.copyright.gov
If I were you, I'd file copyrights for every piece of music I write for these projects. If you don't file copyrights for your music, and your employer has it, they have the ability to copyright it themselves, preventing you from obtaining any further proceeds from it, or from using it in the future. So you have two options:
1. Sell the copyright to your employer for a price described in a contract
2. License your copyright to your employer via a "Synchronization License." (DJ Synchro license)
The first one is easiest. All it takes is a check for $45 and a stamp. Then contact an entertainment lawyer or your local ASCAP board and make sure the deal is good.
The second one might be a bit more complicated, and not as desirable depending on what exactly is happening with this project. Each time your song is synchronized with their animation, they will be required to pay you a royalty, which will be defined in the contract.
Either way, I'd recommend contacting an entertainment lawyer if you're worried about a relatively large amount of money. If it's $1,000 flat, used in an advertisement a few times, no big deal. But if it's radio bumper music to be played frequently and possibly licensed to other companies, go with royalties.