So just create a component for each of the connection you want to be able to place individually, and do whatever you need to do in the schematic to clarify your intent. See attachment. You can create a footprint that is simply a pad, as P1-3 are, and link it to an appropriate schematic symbol. Place them on the schematic however suits your design, and you can even doodle some wires and some wire-mounted terminals to show how the off-board wiring will be done. Or you can place single-wire connectors, like T1-3 (which are PC-mount QC terminals), if that's what you want. The transformer can be done as different sorts of components depending on whether you want it to appear on the PCB and/or in the BOM.