First, you should ensure, that no one is working with aqua. There is at present no way of whether somebody is logged in into aqua.
For offline Client users:
If you are using the aqua Offline Client, please make sure that all executions are completely synchronized.
For JIRA-Sync users:
In case you have configured one or more JIRA-Syncs (see Update Jira Sync), please stop all running JIRA-Syncs using the aqua Sync Configurator before you stop the aqua server. Please note which Syncs have been active. After having terminated the Syncs, please wait ~10 minutes. The Syncs will need this time to terminate properly.
In order to stop your aqua Server, please open IIS-Manager on Microsoft Server.
You should click on aquaAPIPool and stop it with the button on the right hand side. Repeat this process with aquaFileServerPool and aquaWebservicePool.