You can do this, but it’s a little bit round-about. You’ll want to use VADA to build as much of the application as you can discover using the tool, then save the topology as a Distributed application.
Once done, you can import the resultant management pack into SCOM and edit the DA using the SCOM console. Insert a component group for each missing machine, and add the machine to the relevant group. Finally, click the “Create Relationship” button and create a relationship between the machine’s component group and the load balancer (or the tier it communicates with, your choice).
Once you’ve made the changes you need, save the DA and check it’s “Topology” perspective in SquaredUp - it should now include the correct links and can either be displayed directly, or a dashboard can be created back in the “discovery” tab.