As you can see in the picture the refractometer lines up perfectly with the ppt chart on the right but lands just shy of the S.G chart on the left (this is freshwater) should I calibrate it to being on the left chart or the right?
Not only calibrate with a calibration fluid but you need to calibrate to the value you should be seeing. Most solutions are designed for reef tanks (1.0265). Doing so with RODI will give you significant accuracy issues (unless you run your reef tank without any salt)