Overlapping drill hits is a great way to break drill bits and make your fabhouse hate you. Many won't accept such designs.
Not sure which "bonehead" software you're referring to, but in general defining slots can be done in the same manner as defining any other feature on the layout (assuming you're exporting to gerber files):
1. Make a layer in your artwork. Call it something random like "routing"
2. Draw the shape of the routed feature you want.
3. When exporting the gerbers for your design, export the "routing" layer to its own gerber file. Put "routing" somewhere in the file name.
4. When organizing your deliverables for the fabhouse, you should have a top level readme file which lists each file, and describes its content. Make sure this file mentions that you have internal routes (make sure it's clear which ones are plated or non plated), and point out your routing gerber.
5. The fabhouse will looks at the files and figure out how to best create the features (tool size, tool path, etc). They definitely won't use a row of drill hits.