You should better set the two texts at approximatively the same size.
To do so, being them a 6" vs a 9,7", you better use an epub, not a pdf.
Also note that your
PRS 650 display is not like the DXG or the latest Sony T1 / Nook ST / K 4: it's black is noticeably less intense than the last Pearls. You can easily notice this in every comparison you'l find on YouTube.
Quick search:
http://www.youtube.com/watch?v=jHAueOjgmc4 - skip @ 7:07