How are you setting your kemper outputs for tracking?

It's pretty simple in DAW. You create all the tracks you want then save it into a template to load up again for the next project. Each instrument has it's own track. Vocals have their own tracks, and each drum piece has it's own track. However, you can group overheads to one track.

To expand on what BayouTexan said, I'll give you an example of my workflow. I use Cubase and probably have a different audio interface than you, but the concepts should translate to whatever you're using.

I have a 32 channel / 8 bus audio interface (a Yamaha TF5 mixer), so the L/R main outs of the Kemper come into two channels. I also have the direct out signal coming into a third channel. So, input from the Kemper is three channels.

In Cubase, I have a stereo input bus mapped to the L/R outs, and use the L channel of the stereo with the Kemper set to Mono for tracking. (I rarely track in stereo, but if I wanted to I'd just set the Kemper to Stereo out and then use the full stereo input on a stereo track in Cubase.) I have another mono input mapped to the direct out signal of the Kemper.

As he mentioned, in Cubase I've created a template that has a mono audio track for the guitar that points to the L channel input. I have a second track for DI, and its input is mapped to the direct out channel. When I record, I enable both the audio from the Kemper and the DI. If the sound of the profile sits well once the mix is going, then everything's groovy. If not, I have the DI track that I can use for reamping.

So, for regular tracking your template can contain as many rhythm / lead / bass / mono / stereo tracks as you want, with each pointing to the appropriate audio input (SPDIF audio or direct out). I'm sure all the DAWs out there have template functionality so I'd highly encourage you to do a little RTFM to see how yours works. I little time up front with templates makes a huge difference in workflow when you pick up the guitar, avoiding a lot of the back and forth that you mentioned.

Regarding reamping, that's where having a mixer in the loop really helps. My mixer happens to also be my audio interface, but a standalone mixer will get you there as well.

In addition to the channel that captures the direct output of the Kemper for recording the DI, one of my output busses is mono and connected to the Kemper's reamp input (not in front of it right now so not sure what the exact name of the input is, but you get the idea). So, I now have the outputs I use, as well as a DI input, all hardwired to the Kemper so I never have to stop and change patch cables.

In Cubase, I have a mono output set up that points to the mixer output going to the reamp in on the Kemper. The DI track in the Cubase template already points to the reamp output. So, when it's time to reamp, I mute any audio tracks I've recorded, unmute the DI track, and turn the knob on the Kemper to change the input from the front panel to the reamp in. I record arm a new audio track that's listening to the Kemper L/R input, press record, and capture a new audio track from the DI performance. The Kemper L/R is coming to those two channels on the mixer, and that's how I hear the guitar whether playing or reamping.

I'll let more knowledgeable people speak to the challenges of recording multiple tracks in stereo versus mono, but as far as a setup that minimizes your back and forth of unplugging / plugging stuff, here are the main takeaways.

1. Learn how to use templates in your DAW and set them up (I have many, for different styles of music) so that when you start a new song you're ready to go with no fiddling around.
2. If you don't already have one, even a mixer as small as 8 channels in / 4 out will make a huge difference in the convenience of your setup. For example, 3 channels in for the Kemper as I mentioned, 1 for a vocal mic, 2 for the L/R out of your DAW and you still have 2 to spare for keyboards or whatever. My example utilizes 3 outputs. 2 go to my studio monitors, 1 goes to the Kemper reamp in, leaving 1 to spare in an 8 channel / 4 bus mixer.

As I mentioned, you'll have to do some mental mapping of the concepts from my setup to yours, but the basic ideas work no matter what your hardware / DAW setup.

Hope this is helpful.

Similarly to Chris and Bayou, I have a template setup wit pairs of tracks for each take. Each pair is set up to default to Input 5 (DI signal for later reamping if necessary) and Input 6 for Master Mono or Stack depending on how I set the KPA itself. In my case Input 5 is SPDIF L and Input 6 is SPDIF R. This works just as well with analog inputs though.

i rarely need to reamp but the option is always there. In Logic I have each pair of tracks set as an edit group so that if I enable recording in one track the other also ges into record mode automatically. Perhaps more importantly though, if I comp edit a track both the DI and KPA versions of the take get comped and maintain consistency.

My template has at least 5 pairs of audio tracks along with a stereo track for Superior Drummer and a few software instruments such as acoustic piano samples an Alchemy synth.

The pairs of audio tracks covers Bass, Rhythm L/R and Lead L/R but hese can be used for anything else on a song by song basis.