Are you using Extended Feeder Manager or Feeder Manager 2.0? Regular Feeder Manager (or Feeder Manager 1.0, as it's called now) can't really handle truly modeling transmission networks as they are typically giant loops. Extended FM and FM 2.0 can do it, but they take some work to configure properly.
Couple other things to note: you can only have one geometric network per feature dataset. So if you want the trace transmission into distribution, the transmission features will need to participate in the distribution network. If you don't care about tracing through both of them, you can build a separate transmission dataset and build a separate geometric network there.
We have our transmission system in GIS, but it does not participate in any geometric network.