I'm sure when i did mine i just put the key in the ignition and turned it until the ignition lights came on, then removed the power sounder, NO NOISE, no problems.
When i have had the battery terminal off, I only disconnected the NEGATIVE and when i reconnected, for some reason my factory fitted radio was ok but i had to enter the code for the factory fitted CD player to operate.
I didnt know about ECU reseting itself or the window resetting, probably why my passenger window doesn't drop down a little when the door is opened , but i sure will get that working correctly again now i know how 🙂