Unless you plan on running some more modifications eg: performance gear. You won’t need to change the auto ECU, yet.
You should be fine with the auto ECU if you’re only planning on doing turbo back exhaust, FMIC ect. I'm lead to believe (well with S13's anyway) when using the auto ecu in a manual it'll still be injecting X amount of fuel even though the clutch is in, and your changing gears, where as in the auto obviously your foot is still on the gas when the auto changes. If you can follow what I mean?
I used the auto ECU with my auto>manual S13 and didn’t have any problems if that helps.