Yeah throw anything inside that folder. Make sure you name them in the order you want the recovery to flash the files. Like mine are:
001 - Boeffla
002 - Banks Gapps
Also, the OTA works just like normal officials one. Each morning, just click on Check for Updates. It checks the server and builds a new zip by downloading the necessary files. Just make sure you at least have one full build zip (the one you used the first time to flash the ROM is fine) in your phone, so it can build the new zip by comparing it.