It's so hard to understand public transportation system in Japan even for Japanese people, here I tell you what's the best way!
When you visit Japan, I would like you to have good Japanese Sake. But one thing leads you to bad Sake, please check this article to know how to get good ones!
This one of the best restaurant in Kyoto, "Uri" You will have awesome dishes and Sake as well. It's reallly hidden place, contact me if you wanna go!