Thanks for posting!
An upgrade doesn't act as a second license, just a license to replace the version you're upgrading. If you'd like to use both FileMaker Server 9 and FileMaker Server 11 at the same time, I recommend purchasing a full license of FileMaker Server 11. Please see below for the relevant portion of the FileMaker Server EULA as well as a direct link to it.
(f) Upgrades & Updates. If the Software is licensed as a version or feature upgrade or update, then you may only use the Software to replace a validly licensed version of the same software. You agree that the upgrade or update does not constitute the granting of a second license to the Software (i.e., you may not use the upgrade or update in addition to the software it is replacing, nor may you transfer the software which is being replaced to a third party)