Custom network topologies are specified as Python snippets that construct a tree. You can see examples of these in firesim/deploy/runtools/user_topology.py, shown below. Better documentation of this API will be available once it stabilizes.
Fundamentally, you create a list of roots, which consists of switch or server nodes, then construct a tree by adding downlinks to these roots. Since links are bi-directional, adding a downlink from node A to node B implicitly adds an uplink from B to A.
You can add additional topology generation methods here, then use them in config_runtime.ini.