Desktop Director Supports XenApp and XenDesktop. 
In order to support both do following:
- open IIS Manager on Desktop Director Server
- go to Sites > Default Web Site > Desktop Director > double-click Application Settings
- make sure values below are populated

To manage multiple XenApp and / or multiple XenDesktop sites,
configure Service.AutoDiscoveryAddressesXA with the addresses of the XenApp Controllers
for the multiple sites separated by commas;
and Service.AutoDiscoveryAddresses with the addresses of the XenDesktop Controllers
for the multiple sites separated by commas.

Q: Have you succeed to manage in the same time a XenApp and a XenDesktop environment ?
My dashboard only give me the information regarding the XD Site.

A: The dashboard will only show XenDesktop information. If you are just using Xenapp or a combination of XenDesktop and XenApp then you need to search for the user and you will then be able to see the published apps that they are running and view information about the servers they are connected to (provided you have configure WinRM on the XenApp servers)

You will only see real time information for the users that have published apps running. User not running anything = no information.

^^ From http://www.shaunritchie.co.uk/citrix-desktop-director-2-1