Go to Willer express’ English website. From there you can book a bus trip overnight or in the day time. From Kyoto to other various places including Tokyo. Some buses do not have a trunk to put luggage in.
When taking the bus make sure to get there early with a print out of the email with the info. The Willer bus people will be in pink. Make sure it is them and check in. You will get a ticket with your bus number. The people will call out the bus numbers in Japanese. There may be more than one bus leaving at a time. Get on the bus and try to sleep. On the trip they will make one or two pit stops where you can use the restroom. On the bus they informational screens that are in Japanese, English, Chinese, and Korean. This will tell you what stops are coming up. They often have more than one arrival stop so make sure you get off at the right place.