Manual ECU and Auto ECU? The main difference is that in the Auto car, there is also an Auto Transmission Control unit, which the ECU talks to.
If you are referring to the actual auto and manual ECU and not control units: Auto advances up 5 degrees timing when in gear.
No. The ECU in an Auto car has to talk to the A/T ECU. If what you are asking about is "Do the settings in an Auto car equal the settings in a manual car" (ie performance settings), the answer is broadly speaking, yes. However, that does not mean you can get a manual EEPROM chip and put it into an Auto car's ECU. The two ECU's are different. What is different is other things like the gear ratio's, turbo sizes, settings controlling when timing is advanced etc.
If you use a Auto ECU in a manual trans car you have to earth out the neutral switch wire on the ECU plug outlet to fool the ECU advance curve that the car is in gear then reset the timing to 15deg. to make the car idle and run OK.Other wise the part numbers are differant but they will work OK in a manual car.
auto to manual i have changed my twin turbo automatic to a manual gearbox and i have noticed a couple of things with the engine over run when slowing to a stop and appears to be either lean or timming retarded at very low revs ,just up from idle.
If you have the NISTune software on your computer you can open up all the differant rom files in the software program and compare them with each other eg. fuel maps,speed limiters ect. for autos ,manuals, NA,Turbos ect. there are differant 8bit ECU 's for American [federal] Europe,Japanese & Australian cars.