Assuming you bought the kit from Ryan and bought dual end stop cables at the same time, the board will already be flashed with the firmware you need. If you wish to update or change the firmware, V1 releases firmware here. These days, platformIO on top of Microsoft code is recommended for flashing the firmware. There is some documentation on how to use it here.
Where to connect the instrument sensor and how to configure it in the firmware.
If by “instrument” you mean touch plate for the Z axis, then it just uses the Z end stop connection. I’ve never worked with the SKR 1.3, but looking at the documentation, you want to plug your touch plate into the signal (S) and ground (G) pins of the Z- end stop connection. If your board is oriented with the drivers at the top, the Z- end stop connection is the left bottom one.
As for configuration, it should run without changes, but you may want to adjust for the thickness of the touch plate. How/where you make that adjustment will depend on how you trigger the Z Home command.
If you end up needing to flash your board for some reason, you may also have to update the firmware on the TFT. I’ve not used a TFT, but I see talk on the forums about needing firmware updates for TFT screens. Maybe someone else on the forum can comment on this issue.