You already have the best 6" e-ink pdf reader: the prs-650.
But you must Install prs+. This hugely increases the pdf handling capabilities and without it the 650 pdf abilities are let down by poor software (nice one sony!). Read up about the options and explore the various settings under the prs+ settings.
Generally pdfs are best read in landscape mode, but if necessary, zooming is pretty manageable with prs+.
Occasionally I find a pdf that is not quite readable, but 90% of pdfs are acceptable.