Designing a pcb without components, only copper pads and copper tracks connecting each pad to pad
This is very clearly a case for a classical schematic capture program.

You'd simply start out by defining your "pad arrays" as connector footprints (which they are!), then connect the right things in the schematic – and then route the board.

The schematic part is important! It allows you to check whether you've done everything right by abstracting "this needs to be connected to that" from the route the trace needs to take to achieve that. Trying to directly route the board without having defined beforehand what connects to which in a schematic is horrendously error prone – and atop of that, very slow:

when you've made a schematic, your program will highlight the pad you want to connect to, which makes it much much easier and faster to route things. Also, routing helpers are available in many programs – from simple "push and shove a bit" routers to full autorouter.

So, learn yourself a little more about board design CAD tools. I'd recommend KiCAD. It's easy to design your footprints in it, use them in a board and layout that board, and export it for production.