Independent freewheeling is very unusual - the problem is that you then get out of sync and this can cause all kinds of strange wobbling, especially if you have a fairly flexy frame.
You rightly identify the issue of one person feeling that they are barely on top of a gear while the other feels that pedal pressure is too light. The best solution is different crank lengths, but this doesn't come cheap. Highpath Engineering are your friends here - they will re-machine cranks for around £50. They made up a set of 120mm cranks for the back of No.2 tandem for my 6 year old from some old 300LX.
No.1 tandem has a Kiddycrank setup, with a THIRD chain from the left-hand rear up to an extra bolt-on bottom bracket on the stoker seat tube, with dinky cranks. It's possible to fit a freewheel here, but some linkage in the cranks works well to allow younger (4) son to climb on and off.
I think you are doing the right thing, with plenty of communication. The main thing is for the stoker to feel totally confident and relaxed. Keep talking, the rest will follow, and soon you will just know by feeling through the chain. It's really important that the stoker doesn't try to balance the bike - usually you end up getting out of sync and over-correcting for each other. The stoker should usually do signalling for turns etc, as our tandems with two adults aboard certainly need a fair bit of muscling around - lots of steering!
Last one - get a "Yes I AM pedalling" T shirt made up for the stoker...there is a load of people who think it is a hilarious and incredibly original joke.
Ride it or milk it!