We first require that in your process you have a well-defined workflow stage that you consider an item to have started and you have a well-defined workflow stage that you consider an item to have finished. From the workflow data that you upload, then (see above), we take the last workflow stage's date and subtract the first workflow stage's date and add 1 (the 1 makes the calculation inclusive and prevents Cycle Times of 0).
Analytics, however, provides you with more granular control over which workflow stages you want to count as started and finished. As you may have noticed, there is a control called Workflow Stages on our right sidebar which you can use to disable (or enable) workflow stages. We will always calculate Cycle Time from first workflow stage selected on the sidebar to the last workflow stage selected on the sidebar.
You can see the workflow data that is being imported into Analytics via our Source Data "chart," which can be found in the dropdown menu at the top center of the plugin. The first line shows the column names, and every line after that is a work item and the dates it enters each workflow stage. When you enable workflow stages with the Workflow Stages control, you can use this page to see how your data changes.