I am deploying custom apps OTA on a 4.0 server to devices with different carriers. Do I need to create a different software configuration on the admin server for each device?

Not for each device, but for each software package you want to setup. (IE: Admin/user/whatever).

This has been discussed in detail and another thread with the same subject was started a few posts down from this one. Try it and searching for other and you should come up with all the info you need.

Good luck!