I've owned Skymasters with both fuel tank designs, a '69 337D with separate auxiliary and main tanks, and my current 337G with long-range tanks but all tanks in each wing manifolded together to act as one tank. Without a doubt, the older design is far more difficult to operate. It's critical that you understand the design and know how to use it.
Because mistakes here could be life-threatening, I wrote a web page for owners of these aircraft (go to
www.skymasterus.com and click on "Fuel Supply Management"). To give you an idea of potential problems, you can never switch to an auxiliary tank after running the main dry (as seemed to have happened in this accident), because the electric fuel pump doesn't work on the auxiliary tanks. And auxiliary tanks run dry twice as fast (so an engine using 9 gph will drain an 18 gal aux tank in one hour, not two).
To Francisco's question on whether a skymaster be retrofited with the newer system, my answer is two-fold. First, if it's doable it would be enormously costly, because there were lots of design changes in the entire wing tank system and would likely require a large engineering effort to STC the change to retain certification. Second, the older design, although more complex and harder to master, is actually more versatile and offers the pilot greater flexibility and, interestingly, potentially more range (or the same range with less risk).
Ernie