Hello there,
From your question, I get it that you would like to use a JR Pass for 3 weekends (6 days in total).
The JR Pass is counted in conseutive days, which makes it samewhat hard to match to your wishes. Still, depending on where you wish to travel, savings can be had. For instance Tokyo - Osaka or Tokyo - Hiroshima will quickly pay off. Possibly you could also use the JR pass for local travel. It really does depend on what you wish to see and do.
Let me know what you are planning to do and I can give you some better recommendations.
Daniel