Sweetness MACscr. That's great feedback.
The same person did the WHMCS install that also did the web site itself. I wouldn't call it a simple integration. I do digress, we were working against time limits. It's something we'll have time later on to work with and improve upon. For the time being, the way we have it will have to work (and does work out pretty well, for all practical purposes). We'll have to wrap the site around it a bit more in the future.
Any suggestions on how to go about that (not from a technical aspect but from a design aspect) in regards to what to do with the links / login box / search box on the left side?
In regards to the default Kayako support icon being there, that's a new one on me. This morning I had placed one there that was custom built and for some reason it grew legs and walked off on it's own (although I did tweak some things in Kayako this morning but I can't imagine that it would cause icons to be overwritten).
Oddness.