Best way to split guitar to signal to into 2 inputs of Axe FX III

If you've got a buffered pedal before the split, you should be fine. Y cables put the input impedance of the two devices connected to it in parallel, which reduces the input impedance by at least half. This loads the pickups in your guitar more and can lead to tone sucking and signal loss. However, if you have a buffered pedal before the split or are using active pickups, the impact of the split on your guitar's tone is negligible.
 
so, after some pondering - I still don't think you need dual input which is going to be awkward + it may be tricky to get the exact same signal coming into the grid on both due to special input sauce on input1 only. As in the example below, if you go out L/R through loop3 (I use loop3 because it is unity gain so best for pre pedals) into your mono OD pedals with your clean amp OD pedals in loop3L and your dirt amp OD pedals in loop3R (same separation / order as you would set them up with split input), then back in to hard panned amp blocks 1 and 2 set up for Input L and R respectively, and then into a stereo hard panned cab block, then output1 to your DAW will yield your Clean L with active clean OD pedals, and your Dirt R with active dirt OD pedals. L/R could be separated / mixed in DAW (or in the preset, ie if you wanted the two going out separately (add Vol blocks to send L to out1 and R to out2)).

methinks... maybe?

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Don't put the effects loop in parallel like this. It will make any pedals you put in the loop basically have a 50% wet/dry mix. It will also cause phase issues between the loop and the parallel dry path since the loop has extra D/A and A/D conversions. Put the In 3 and Out 3 blocks on the same row or delete the cable that runs between the comp block and the shunt block to its right in the same row to remove the dry path.

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Don't put the effects loop in parallel like this. It will make any pedals you put in the loop basically have a 50% wet/dry mix. It will also cause phase issues between the loop and the parallel dry path since the loop has extra D/A and A/D conversions. Put the In 3 and Out 3 blocks on the same row or delete the cable that runs between the comp block and the shunt block to its right in the same row to remove the dry path.

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Yes, I should add when I used to do this i would used a multiplexer to switch between a row of shunts vs the loop of output/ input 3
 
No need. If you put the Out and In block in series in the same row and connect them with a cable on the grid, you can just bypass the In block to bypass the loop completely. All of the In blocks pass the signal from their corresponding jacks when the block is active and when they are bypassed they pass whatever signal is fed to the in block on the grid.
 
Don't put the effects loop in parallel like this. It will make any pedals you put in the loop basically have a 50% wet/dry mix. It will also cause phase issues between the loop and the parallel dry path since the loop has extra D/A and A/D conversions. Put the In 3 and Out 3 blocks on the same row or delete the cable that runs between the comp block and the shunt block to its right in the same row to remove the dry path.

View attachment 115447
my bad - I usually put a mixer block there and took it out for simpler illustration (forgot to remove the link - doh"). I like using the mixer block because it gives me a lot of flexibility with loops with almost no extra CPU usage - so I tend to always set up my loops this way whether I'm using the mixer for additional features or not.

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