Ok I found out how, but now the next step is to update the template within the management pack ??
#Create template property object
$propClass = [Microsoft.EnterpriseManagement.Configuration.ManagementPackObjectTemplateProperty]
$propObject = New-Object $propClass
#Add new item to property object
$propObject.Path = "`$Context/Property[Type='CustomSystem_WorkItem_Library!System.WorkItem']/Id$"
$propObject.MixedValue = "SR{0}"
#Add property to template
$template.PropertyCollection.Add($propObject)