Craig, I apologize but we have absolutely no experience with JD Apex. Farm Works supports standard data file formats with the Ag Leader Advanced text file format along with Arc View Shape Files. Shape Files have been a standard file format for virtually every mapping package used in ag. You can export any map from Farm Site in a Shape File format. The only drawback is that most ag software packages treat shape files as "general" maps. What this means is if you import a yield map as a shape file, it will be recognized as "general map data" and not yield. This means that you can display the map and assign legends to it, but you likely won't be able to use specific features for yield such as filtering, applying delays and other features. We added the export for the Ag Leader Advanced (text) format to add a way to export data in a format that's recognized by most software as yield.
Hopefully someone reading this will have had some experience with Apex and they will add a response. Otherwise the best thing to do will be to contact John Deere's tech support department.