I don't know enough about Zend Server to say for sure (e.g. I've seen someone manage to wedge CI into Joomla before), and while I'm sure it's possible, I imagine it would require a lot of tinkering. What you can do is pick and choose your favorite bits of CI or Zend and reuse the code as libraries. Are you being forced to use Zend but would prefer to use CI? If that's the case, I feel for you, but I'm not sure the best solution is to use two entire frameworks with all the overhead that comes with them...it would probably end up being really unwieldy.