For me the bottom line is recording flexibility and live reproduction -- meaning, getting similar sounds live that have been recorded. Also, simplicity is important.
I use the Axe-FX II mainly for effects and the Kemper for the amp/cab sim (both recording and live). The guitar plugs into the Axe and the Kemper is in the effects loop of the Axe. I use the Axe for the various stomp box and pedal effects at the beginning of the chain (compressor, drive, wah, phase, etc.), insert an FXLoop block next in the chain (which is the Kemper Amp and Cabinet), then I can add stereo effects after the FXLoop (Kemper). The beauty of this is for recording, you can record both the output of the Axe AND the output of the Kemper. The output of the Axe will include the pre-amp chain, the Kemper, and the post-amp effects. The output of the Kemper only includes the pre-amp chain. You then have the option of adding post-amp effects (plug-in effects) which is what I usually do for recording and mixing anyway. If you get real crazy, you can even get another mono signal out from your pre-amp effects chain (Output 2, Right) and do something with that signal (to another amp/cab sim setup or whatever). Oh, and for live, you would use the Axe output which will include the post-amp effects (usually stereo effects like chorus, delay, reverb, etc.).
Another cool thing about this setup is that you don't have to swap cables. If you don't want to use the Kemper in the chain, just don't insert the FXLoop block and use an amp/cab from the Axe arsenal. I sometimes add another parallel amp/cab to the chain in the Axe profile to get a stereo amp tone. You then can experiment with different mics, pan, mix settings in the Axe - lots of flexibility.
Here are the connections for this rig:
** Guitar to front INSTR input on Axe-FX II
** Axe-FX II Output 2, Left (rear) to INPUT on front of Kemper
** Kemper Monitor Output (rear) to Axe-FX II Input, Left (rear)
** Axe-FX II Output 1 Stereo (Left and Right) to Recording Interface
** Kemper Main Output stereo (Left and Right) to Recording Interface
You have to use the proper I/O settings on the Axe:
** Output 1 Mode Stereo
** Output 2 Mode L+R (or L->R)
You may also have to pad the outputs on the Axe to reduce the noise floor. I have mine set to 6 dB on both Output 1 and Output 2 -- works very well.
Let me know if that helps or you have any further questions. I've been an Axe-FX user for quite a while (Ultra then II) and I just added the Kemper to my rig this year. I find that the Kemper gives you some additional amp/cab 'flexibility'. Both units represent leaps forward for signal processing -- both are phenomenal boxes!
Steve