The only difference in a Point to point communications verses a point to mufti-point really is if the data needs to be sent to a specific node or if it can be sent to All nodes.
To send to a specific node, you use the 64 bit MAC address as the source address and the address in which you want to provide the transmitting module. That address is what the transmitting module uses in the DL and DH fields before sending the data or in the address fields of an API frame.
For sending to all nodes, the destination address instead becomes the Broadcast address or FFFF.
By default, when a Zigbee network is formed with XBee ZB modules and products, the Coordinator (AT) is in Broadcast mode and all routers and End devices are in Unicast mode back to the Coordinator. In this case, since you are using API mode, your choice on if you send a Unicast message or a broadcast is completely up to you and the message you send.
The choice of using Broadcast vs unicast is really dependent on if you are using an existing protocol or if you want to create your own. If you are using an existing protocol, can tolerate other devices hearing the data and determine if it is for them or not, and you are not trying to scale up to more than 30 - 50 nodes, then Broadcast could be fine. If you are however, developing your own protocol or will be having large amounts of nodes, I would strongly recommend using Unicast addressing.
The choice to use API mode vs AT mode is determined for each module and not as a network in whole. The reason for that is that API mode and AT or Transparent mode is really how you are going to interact directly with that specific modules UART only.
Finally, the version of XCTU you choose is really more dependent on which one you are more comfortable with.