Scripting startup or restart of web sites

We are using an iSeries for our database and to run code. We have Windows servers for presentation, including two web servers and one deployment server. When the backup runs on the iSeries, it causes lock problems and the web sites stop running. I can use Server Manager to restart the sites (sites are e.g. JDV910-Enterprise One HTML Server or JDV910 BSSv-Enterprise One Business Services Server.) But that is a real kludge. We need to be able to shut the sites down, then after the backup completes start the sites, all with commands in the backup routine. I have searched