The amount of time you collect data depends partly depends on the conditions you're seeing. If it's mostly good, then you might need a bunch of time to catch a bad period. If it's mostly bad, you might need a bunch of time to catch a good period (best results show good some of the time, bad some of the time).
You don't need to stop whatever else you're doing when you collect data - just start PingPlotter and minimize it. Look at it again when you're having issues so you can add a comment to the data. When you have enough data for a compelling case, then save it off and send it in.