CalTopo + Orienteer
CalTopo is an incredible tool for making maps and courses. I use it all the time to create maps for races as well as courses. The "Pro" plan lets you make 400dpi 12x18in maps with very little fuss. Incredible! I've made Orienter compatible with CalTopo GeoJSON, so you can import and export both ways, depending on how you want to go about it.
Importing and exporting is quick and easy. In order to load them into Orienteer, open up the course editor, go to the "checkpoints" section on the left, and you'll see an "import GeoJSON" section. Drag your file in, pick a default radius for the checkpoints, and hit Import.
To export GeoJSON for use in CalTopo, there's a "GeoJSON" button below the checkpoints that you can click. This will download the GeoJSON representation of the checkpoints.
Hope that helps (And shoot me an email if it doesn't!)