I think you missed something

Everything should still work the same way it did before you integrated the two together. You are only adding a few files to modernbill to allow kayako to take over the modernbill support system. You should still be able to login via web using kayako to add staff/change settings/ect.. and you should still be using your windows app to check tickets/chats. Modernbill still works the same. The only thing that changes is the ticket system in modernbill.. It simply redirects to the kayako ticket system so things are gravy for yourself. If you had kayako and modernbill running smoothly before you integrated the two then you changed permissions on something or edited/replaced the wrong files.