To start off with, If your using BlackBerry Desktop Manager 6.0 (the newest version) you will be unable to sync the CA cert. onto the device with it, It's currently unsupported in 6.0 and is "targeted for a future DM6 release" according to RIM.
Originally Posted by numberonebun
Supported files to be synched onto the BlackBerry device to upload a new certificate are .pfx, .p12, .cer, .der, .crt, .cert, .p7b, .p7c, or .key files.
1. Connect your device to your computer.
2. Open BlackBerry Desktop Manager.
3. Click Synchronize Certificates.
4. Click Import Certificate.
5. Click a certificate file.
6. Click Open.
If even with these instructions, and DM5, your still unable to get it on there, The option may not be available (especially if your device is connected to a BES, it may have been disabled by your BES admin).