I hacked my 6exa and removed the transmitter board all together then connected the wires to the 2.4.
If your not going to or can't remove it then I would disconnect it so that it it doesn't drain power from your batteries, or poss cause any probs with 2.4... don't know if it could? You can use the plugs from servo extensions if you want to be able to swap from 2.4 to 40 at any point.
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