Does My Company Need To Code Sign with Two Digital Certificates? Apple Developer and EV Certificate?
Here is what the Apple Documentation says about this in the Developer ID section: "You can distribute your Mac applications outside of the Mac App Store by using Developer ID. Signing your Mac applications, plug-ins, and installer packages with a Developer ID certificate lets Gatekeeper verify that apps are not created by malware developers and haven't been tampered with since they were signed." Here's the link: http://developer.apple.com/programs/whats-included. Click Learn more in this section for details. 

According to the documentation approved developers can request the Developer ID and use it to build certificates and sign app files. From what I read it appears you will only need the Apple certificate. I plan to do this when I'm approved as an Apple Developer.