Check out the video at BICG http://bicg.com.au/index.php/power-pivot-add-a-secondary-axis-to-a-pivot-chart/.
You have a Percentage measure to add to your chart and you want this to display on a Secondary axis (because the primary axis has counts and the range between the two is way out of proportion).
First add your percentage measure to the Values section in your field list. You may see your percentage value as a small horizontal line compared to the other bars in your chart. Just left click this one to select it as pictured.
Now Right click and select “Change Chart Type”
Now put a tick under Secondary Axis for your Percentage measure only.