When I converted my 3EQ to a 2EQ, I used the same 4 hole plate...vol, treble, bass and jack which is standard for the 2EQ arrangement anyway.
I used the body jack to run straight to the pickup (for a passive alternative to the active). Sounds good and is a stand-by just in case the battery gives up at the wrong time. When the jack is removed from the plate the 2EQ the battery is turned off and you're not wasting power. I also wired the body jack to disconnect the 2EQ from the pickup (when the lead is inserted) to avoid any interaction between the two modes.
Of course, the tone settings for the new passive alternative can only be done at the power amp.
I did a wiring circuit for the conversion if you want it.
If you don't want passive, the idea of running both jacks in parallel is a good idea.