I had the same issue, but with CentOS.
It really was no problem. Just go through the process and follow the instructions carefully. Pretend that it is a clean minimal install.
If you have issues when completing the install, note those issues, you may need to uninstall ISPConfig and go through the process again noting things to change as you go, ie: apt-get remove sendmail (as an example) before you continue with the walkthrough.
Note, if you are using godaddy's vps, you have to use 'relayhost=['servernamehere']' as the relay host. Remember the brackets, they are important.
I was unable to find a mod_ruby.so for CentOS/64 bit and I skipped configuring Apache with Ruby with no apparent consequences outside of being unable to offer Ruby as an option.