I see that a lot of people end up to my blog by troubleshooting Appcelerator cloud service. I have written about this in this post: Push Notification tutorial with Appcelerator Cloud
But to say it shortly again. You cannot upload .cer file but you will have to make .p12 certificate. You can do this using Keychain Access on your mac.
You will have to right click on the certificate and choose export… from the menu.