nlapiScheduleScript puts an instance of the scheduled script into the queue for scheduled scripts. nlapiYieldScript is the api for pausing your scheduled script long enough for governance limits to reset.
You can use both the difference being that if you use nlapiYieldScript you do not need to keep track of where you stopped or “reset” you script. If you use nlapiScheduleScript, you will need to keep track what record or line you are currently working on and pass them as parameter values in the nlapiScheduleScript call.