its basically the same as the topic title. would it be possible to run both n the same server without damaging each other?

Yes.

Thats not to say you wouldn't see better performance if you were to separate the softwares, but they will work either way.

so they will work without me having to set up a seperate virtual enviroment? as i dont want to crap up my cpanel as ive got like 50 resellers on there.

I dont think this is a good idea.

Cpanel writes to the ftp, mysql and email etc. configs, Ispconfig would then try and edit them potentially damaging the configs. This is my understanding of it, Correct me if im wrong.