It sounds like you did the right thing; CabWriter doesn’t really know anything about the type of slide, only the info in terms of cabinet depth, hole spacing, etc. Could you email me your file at email@example.com, or a link to it, so I can take a look? It might be something simple, or maybe you’ve stumbled on a bug.
Of course, you can draw holes at any time using SketchUp on the carcass sides and they will show up in the DXF. You don’t have to worry about the layers; simply draw the holes in the carcass part. If the hole is all the way through the part, CabWriter will automatically put it on the “Construction Holes” layer in the DXF, and if it only goes partway through, it’ll be put on the “System Holes” layer. I’ve done it manually at times where CabWriter can’t do it for one reason or another.