If you read ULA's "Aft Bulkhead Carrier Auxiliary Payload User's Guide" found here: "http://www.ulalaunch.com/Products_AtlasV.aspx" , you'll find details about the requirements for Auxiliary Payloads (AP). Primarily, it says the Auxiliary Payload Coordinator (APC) is responsible for making sure the CubeSat meets ULA's requirements for Atlas V launches.
This means that the APC is going to come up with some plan with the CubeSat developer that ensures satisfactory payload capacity for the loads that it will be put through during transport and launch, the electromagnetic interference, and the thermal environment, in addition to making sure the CubeSat doesn't damage the Centaur with debris, outgassed materials or any other contamination.
This is what I gather from the user doc, I'll know better after a year is through, since my team's CubeSat (BYU PIC 1.0) has an offer to launch with the WorldView 3 satellite next year.