Defining wire jumper inside IC in software
If though the PCB is single-sided, pretend it is double-sided and route the trace just up to the conflicting trace, and add a via. Do the same for the other side, where the original trace starts up again. Then put a piece of wire between the two vias on the opposite side of the PCB.

If you are only using through parts, then use can put all of the traces on the bottom, and components on the top, in a traditional component side (top), solder side (bottom) scenario. In this case the jumpers I referred to will show up on top, along with the components.

Here's an example; note the red and green jumpers: