since it is a modeler, just think of it as amp, cab and mic in a box.
first, I'd disable all effects, so that you just have the amp model and speaker sim active.
then just connect as described in the manual.
short version: guitar -> Profiler -> Profiler's Send -> modeler In -> modeler Out -> Profiler's return
Yeah it is super easy! Make sure the noise gate is off also.
Only problem I had is that with the noise gate off some patches would be too noisy to profile that had a drive pedal (one of my pet hates with the axe-fx was the only way to get the gain levels I wanted I'd have to use a drive pedal, and with amps in real life never had that problem hence mimic not being accurate)
What I do in the above case is turn the drive down or removing it and then adding one on the kemper
The great thing is in my experience it will have less noise than the axe-fx and now you don't have the fan noise either!
What was the solution? I'm having same problem, can't hear reference amp! Please help!
The output of the reference amp can be monitored through the outputs of the PROFILER. This way, you can switch between listening to the original reference amp signal and the profiled version using the soft buttons in the profiling mode. In fact, we recommend that in order to avoid any confusion between what you are hearing and what the PROFILER is profiling, the reference amp should only be monitored using the PROFILER.
Evaluating the Profile
Once the Profiling procedure has ended, you can make the first A/B comparisons between your reference amp and the new profile. Use the soft buttons to switch between the reference amp and the PROFILER/ profile
A/B comparison to “Kemper amp”, and the to “Reference Amp”
Thanks for your response Paults but I'm still having problems hearing the AXE as a reference amp. I have it set up the way Layne81 has his setup a couple posts up above. I tried various soft buttons and the output menu pages for volume. What specifically should I be doing to control volume? Sorry in guitarded
No need to apologize - I've only profiled amps, so I was just quoting the manual 
From what I remember, there are soft buttons that allow you to select the orginal amp or profile.
The output of the reference amp can be monitored through the outputs of the PROFILER. This way, you can switch between listening to the original reference amp signal and the profiled version using the soft buttons in the profiling mode. In fact, we recommend that in order to avoid any confusion between what you are hearing and what the PROFILER is profiling, the reference amp should only be monitored using the PROFILER.
Evaluating the Profile
Once the Profiling procedure has ended, you can make the first A/B comparisons between your reference amp and the new profile. Use the soft buttons to switch between the reference amp and the PROFILER/ profile
A/B comparison to “Kemper amp”, and the to “Reference Amp”
But what if your reference amp is in the same room?!
Ideally, it would not be in the same room. But, you could use headphones.
Or, just make several profiles, and skip refining. Pick the profiles you like the best 
Or an iso cab could be the way forward...! 
An ISO cab can work, if it is a good sounding cabinet (or, if you leave all your amp knobs set for your regular cabinet, and just make direct amplifier profiles).
