Well what you have to think about is what do the programs do??
They do EXACTLY what you do with an E6B, BUT they are able to do it more accurately because of the technology involved.
I feel if you can't manually plan a flight then there is something wrong.
Even on the ailriners there are loading charts, flight planning charts, weight and balance, V-speed calculations and what not in the AOM manuals. This is even with the FMC that does all of the calculations for you.
It would be important to be able to plan a flight manually, but as long as long as you are able to back up yourself with a manual way to do it there should be no problem.
The problem of the automation has been recognized by the airline industry and in at least the 747-400 manual there is a note describing this. With the automation comes complacency on the part of the individual relying on the computers to do the work and just punch buttons. There have been numerous airliners with GREAT FMC and MCP integration--2 PILOT CREWS, but have STILL managed CFIT( controlled flight into terrain).
The automation is fine but you need to have an underlying understanding as to what is going on.
I read an article in FLYING a while back about GPS and there have been students who went for there SEL check ride. They turned on the GPS after starting the engine and the examiner reached over and turned it off and the student could NOT fly the plane, UNBELIEVABLE!!
I was just thinking about something else that is relevant.
During my college career, I had a math teacher who was phenominal. He could do complex arithmatic in his HEAD, AC analysis and such. Someone asked him how does he know if the answer is correct. He said determine if the answer is logical. Think back through the problem and determine if the answer could be accurate or even close.
This has a direct bearing on your question because if you know how much fuel burn your airplane produces and you know the wind, then you should be able to come up with a best guess as to what you should expect. The flight software has to know this in order to do the calculations so accurately as well as interpolating the winds and what not. HOPEFULLY this was helpful.