While I'm a Cacert assurer as well, it's a while since I've done this, as I use a homebrew multidomain on 1 IP setup.
The ISPConfig technique, is that you take the Certificate and paste it into the text box provided for the site under the SSL tab that appears when you enable SSL.
I just have a nasty suspicion that you should use a CSR generated in the same place (the SSL tab) for the certificate generation. i.e. generate the signing request there, and cut and paste that into the CaCert form.
ISPConfig then parks the certificate in the correct place for the site, and sets up the paths etc for the secure connection in the Vhosts file.
Thinking about that, that probably takes care of the key, as the ISPConfig key is used to generate the CSR.
You may need to grab the CaCert certificate chain file as well and put it in the ssl folder.