Hi Ronnie,
You have quite a few choices..
By default, KonaKart will install so that it listens on 8780. Your existing tomcat probably listens on something else like 8080 so they can both run together without problems. You should check in the two server.xml files to ensure you don't have port clashes.
You could link your existing site to the KonaKart tomcat if you like or you could copy the webapps from the KonaKart installation across to your existing tomcat installation. (or you could create WARs of each, then move these, if you prefer).
Another alternative is to move your existing site across to the new KonaKart tomcat...
I don't know the level of integration you're seeking to achieve.. You might find running KonaKart separately in its own tomcat advantageous as it would allow you to run it on another machine - plus it would be easier to diagnose any problems because it would be a vanilla installation. (If the tomcats are different versons and have conflicting jars, you might like these to be as independent as possible!).
There are many considerations and options...
Ming