We have found that we can usually harvest the honey without the bees noticing us at the back of the hive. Nevertheless, it is best to cover the jars with mesh or plastic wrap, or better still, make a closed system. This can be achieved by simply making a hole in the lid of a jar for a tube to go into. Just make sure that there is a little bit of space for air to get in, otherwise, it can cause the honey to back-up in the honey trough.
If you are harvesting several frames at once using a larger container, you can make holes through the lid for each tube.