xendesktop and xenapp farm on the same WI

You can can create multiple xml virtual servers; in your example, one for your xenapp farm and one for your xendesktop farm. Add each vs ip address as a server farm on your web interface server and users will see both their desktop and application resources. You do not want to mix farms within a single xml vip, doing so would give the users their xenapp resource or their xendesktop resources depending on which xml broker the user was sent to in the pool.