There is no direct or official license upgrade process.
However, notice that System Edition is functionally Logic Edition plus (Embedded Development Kit ,Software Development Kit & System Generator). http://www.xilinx.com/products/design-tools/ise-design-suite/index.htm
It is possible to just buy an Embedded Development Kit, Software Development Kitand System Generator licenses. Below is the link which will give you information on additional standalone tools for thosewho wish to purchase one tool at a time based on their usage.
So, assuming you bought this with the same type of license (e.g. your purchased logic edition is node-locked and you have purchased a node-locked for additional tools), cut the license to the same machine. The composite licenses will give all of the functionally of a System Edition license. In the event that you use floating license type licenses, the use of separate licenses will give slightly more flexibility since there will be two separate increments available to be checked out by different users for the different components (a single Edition license has one increment associated with a package of bundled components).Questions about purchasing should be directed to the customer's Xilinx product distributors.