How should I set up my design file for a sandwich business card?

Set up a sandwich card file the same way you would any business card, then let production handle the layered construction. Your artwork covers the two printed faces, while the colored core is selected as an option rather than built into the file.

Design the front and back as you normally would and keep important text inside the safe zone. The bonding of the three layers and the final trim that reveals the colored edge happen in production, so you do not need to account for the core in your artwork.