Yes, you can use different certificates for different domains, even if they come from different certificate authorities.
Please note that in order to use different certificates with different domains (regardless if they are from the same CA or different ones) with a server that only has one IP address, your web server software must use a feature of SSL/TLS called Server Name Indication, which is not available on Internet Explorer for Windows XP, the stock Android 2.x browser, and some other very old browsers.