my 88 gxl has the safc set to 6 in 6 out on the flapper door....
 

when i change it to 5 in 5 out will i have to re adjust my fuel settings?

i never did quite understand the whole in/out adjustment but i would imagine it is the voltage in vs voltage out, since it is a 5 volt reference signal and is going to be unmodified is what i assume they use it for.

switching it from 6 volts to 5 volts means you likely will have to make some minor adjustments to compensate for the new linear tables.

Ya im not to sure either, it explains it in the manual pretty good.

Although I found the engine ran no different between the 2 settings. If I had it set to 5, 5 or 6, 6.

I wouldn't set it wrong though there is a reason APEXi tells you to set it that way.

You have a S4 ECU so you should have it on 5 - 5. I wouldn't worry to much about having to change the fuel setting when changing it to 5 - 5. Just start it up and see how it runs. You can always bring the corrections down or up a few notches depending on if you have spots richer or leaner.