Hi Jim,
Flash cartridges should be good for life. The chips inside are typically rated for 100,000 full erase/write cycles per cell. In any case, they are warrantied for life by me. If one ever fails it will be repaired or replaced at no cost.
As for loading, you should check out the Maxflash Studio software here:
http://www.atarimax.com/flashcart/Scroll down to the bottom to download the studio software. You can use that to create multi-carts with on-screen menus, then flash them using the USB programmer from within the software. There is a short movie on the site of using the software to create a cart, as well as some written documentation.
The USB programmer is relatively easy to install. Drivers are provided on CD for all versions of Windows from Windows 95 all the way up to the newest Windows 7, with full 32-bit and 64-bit support.
Steve