I bought a Jeppesen Flight Computer 20 years ago, and I STILL use it for my pre flight planning, just to give a heads up on potential drift corrections.
However, I use all available means to create a plan. I have used Navbox and got a plog print out, and I have also used a handheld GPS to build the back up route. This has the benefit of giving me highly accurate true headings to double check the manual plan that I have created using the CAA Chart/Whizzwheel.
To address the other issues, I normally plan my flight using obvious geophysical waypoints and fixes, but naturally incorporate into the plan any handy VOR/DMEs or NDBs to add extra accuracy.
For me, part of the fun and skill of flying is doing everything necessary for the safe conduct of the flight manually.....
Blue skies