As far as I know it’s not possible to select which metrics to use in a custom variables graph. For example, I have 3 custom variables defined, Agent, Email and Page
http://mymobilepatron.com/cache/piwik-set.png
Clicking graph gives me a graph of how many each of these have as an aggregate total.
http://mymobilepatron.com/cache/piwik-result-1.png
What I would like is a graph of one of the 3 custom variables such as Agent > Actions as selected here
http://mymobilepatron.com/cache/piwik-detail.png
To show a a graph something like this: