Since I have no components, its a little hard to start with a schematic.
Connect with VIAs? I think you MAY have your terminology wrong, A VIA is a very small plated hole connecting one side of a PCB the other. You need pads for connecting a PCB to a PCB.
What you do is add terminals to the schematic and connect them in an interconnecting schematic.
You are kind of thinking of component wrong. Find a component that give you a hole pattern on the PCB that you want and add it to you Schematic, just because you are not going to mount on the board does not mean that you can not use it to lay out the PCB for what you need in holes spacing. You can then wire any of those component on the schematic for any traces you want.You can make components for your needs like one for a rework area.