If you post a packaged workbook (.twbx) file, someone can help you figure this out. We just don't have enough information from your original question. You can mock up a scenario using sample data and post that here if your production workbook is sensitive. Its very difficult to describe a solution for such a visually driven tool.
We would need to know what the measures are you want to use, and what measure you want to compare them to. Typically, stacked bars are used to show different representations of a dimension's part of a whole (like customers that made up all sales, etc.) so I'm not sure what you are trying to accomplish.
Please see: http://community.tableau.com/docs/DOC-5065
It is possible to use measures to represent chunks of a whole in a stacked bar, if you can convert them to dimensions first. Attached is a poor example, showing Order Quantities representation of total sales. However, there's almost certainly a better way to show this information and I would never build this chart unless there were only a few order quantities.
You may also want to see: Creating a Stacked Bar Chart using Multiple Measures | Tableau Software, although I'm not sure how much help it will be in your situation.
% of another variable: try quick table calculation "Percent Difference", change Compute using to "variables field name", and set the Relative to "Previous".