The Quality section will count toward 60% of your overall score. Another way to think about it is that it will account for up to 60 of your possible 100 points. For scoring purposes CMS will use 6 measures at least one of which must be a high priority or outcome measure.
Clinigence will report all selected measures and CMS will calculate the best possible score for the submission. In the past you received full PQRS credit just for reporting. The percentages didn't matter. Now the percentages matter and more importantly the percentages compared to your peers' percentages matter. For example if you score 95% on a measure but your peers generally score 98% that measure may not be a good one to count. Whereas if you score 25% on a measure but your peers score 10% you would receive a higher score than you would for the 95% measure. It is not an easy or intuitive calculation which is why we will submit all measures to ensure that the best 6 are submitted.
The attached benchmark, calculation, and scoring documents can be used to calculate your score. Each of the 6 measures can contribute as many as 10 points to your Quality score for a possible total score of 60.