What I am trying to do is get an "all sky" camera on my mount for the imaging session. So I would be looking at running my regular imaging mount and guide camera with kstars/ekos. I am then wondering if it would be possible for me to use some additional capture software that is different from kstars/ekos to capture on my all sky camera. 

Thanks

If the All Sky Camera is running separate software and has an independent connection to your computer then I can't see any reason for it not to work. 
Hopefully your computer is powerful enough to cope.