As long as flrig/fldigi is accessing the transceiver, the only thing you need is a setting that uses the correct CAT command.
No other menu setting on TS-480 will select the input, just the CAT command.
It depends on what CAT method you are using.
A. If you are using rigcat, the TX1; command is already configured to be used in the xml file ( https://www.w1hkj.org/files/xmls/kenwood/ ) so there is nothing to set.
<COMMAND>
<SYMBOL>PTTON</SYMBOL>
<SIZE>4</SIZE>
<STRING>TX1;</STRING>
</COMMAND>
B. If you are using hamlib, you should enable the "Audio on Auxiliary Port" in Fldigi "Configuration -> Rig control -> Hamlib"

C. If you are using Flrig, the "Mic/Data" button must be pressed in order to be lit indicating "Data"

Submitted by Haris, SV1GRB