I have frequently deployed Kentico along with other apps. Usually do the second app as a Virtual Application. Then in the Web.config, above the
<system.web> we place
<location path="." inheritInChildApplications="false">
Your Web.config will have to merge. We have also had to move a few DLLs sometimes from the BIN of the Second App, but to the /bin.
Security for the 2 apps. Good question. Without knowing what you are combining with, it is hard to say. We have done BRIDGE pages that SSO between 2 app before. We combined an Old ASP app with Kentico and had to create a SSO layer.