I use the 'Export for Production as an Etchable PDF' method.
If you have a long line of continuous holes like a header, you might have to scale it a touch to get the dimensions perfect, so do a test print.
When I used thin white gift wrapping paper I printed at the std darkness, because when you iron it it squashes out the tracks wider than they are supposed to be. Now I use the yellow wax paper from eBay and that needs to be set at the printers darkest.
I also put a via with a 0.5mm hole on every connection, because after tinning it provides a good drill guide to centre holes - the 0.8-1mm holes allow the drill to not find the centre -.
On this board I'm going to sand the gloss off the top, for adhesion, and toner transfer the silkscreen as a part guide.
Also don't use cheap eBay PCB because the copper tracks seam to fall off easily after etching.