MESHdesk is used to centrally manage various Batman-adv based mesh networks and APdesk is used to centrally manage single Access Points.
If you just signed up a restaurant chain and need to supply WiFi country wide to their 75 locations, then APdesk is your friend. These locations are not large enough to justify a mesh network so you just place one Access Point in each branch. But you still need to centrally manage the Access Points deployed in each of these branches. APdesk allows you to manage these distributed Access Points as one group.
The MESHdesk firmware has various modes it can be set to by using the MESHdesk Node Config Utility.