Holley Sniper EFI

Hi Johnny, I'm still having a few issues, haven't been able to play with the car much due to bad weather here. I'm looking at replacing the manifold with a single plane one I had in the shed, going to see if it makes a difference. I noticed too, when I make adjustments with the SD card out and on the computer software, I go to put the SD card back in the car and some of the new settings that I changed don't seem to take. Do I need to make these adjustments with the USB dongle to the Sniper unit while in the car?