If all else fails, read the manual!!!
Here's a PDF of the wiring instructions for SAFC (not sure what AFC you have, go to apexi.com -> support, and select your AFC from the list of manuals)
http://www.apexi-usa.com/pdfWiring/7.pdf
Take a look at this pic:
The yellow and white wires from the AFC *intercept* a signal going to the ECU. This means that you disconnect the yellow and white wires and *RECONNECT* both sides of the original ECU wire back together. If you don't, the MAF signal won't get to the ECU. The other wires are basically spliced into existing wires, or are ground wires. You can just disconnect those, but be sure not to leave any exposed wiring when you're done. Cover up anything w/ electrical tape if you have to.
*EDIT* I didn't notice you had mentioned you have an AFC Neo before I posted. Neo should have the same wiring, but check out the manual to be sure. Also, you can turn the correction factors off on your AFC and it will go back to stock settings. Or just zero out all the rpm points. Either way you can run stock airflow settings w/ the AFC in the car, at least until you get a chance to disconnect everything.