It seems to me that it was connected up exactly the same way as the 12.6 V "bucker" was, with a choice of half the secondary winding or the full thing. What was the transformer that you have used? The 166N12B? I don't really want that much "drop" in the two steps. I'd like to drop 4-5 V for the first step, and 9-10 for the second.
My speculation here was that the VA rating matters more than the secondary voltage spec, but if @robrob used transformers of two different voltages, that conclusion is problematic. I guess I have to get the Triad 80 VA transformer out and rig it up to test the output when it's connected to wall voltage; and then load it by connecting to an amp and see what happens.
Basically, the 6.3v and 12.6v transformers are wired as a autotransformers (AT). Take a look at the Wikipedia page on autotransformers for details and formulas. I installed an AT in my '63 vox ac15 that was eating el84's, lowered the HT and it is much better now.
You are correct in that both the voltage and va of the AT will effect it's output, but if you are within +/-5v of your target line voltage you shouild be good. Looking at robrob's web page, selecting a 48va transformer is enough to power a 5e3. If you want to apply this to a higher wattage amp you will need a trans with a higher va. But I see no downside to usnig an AT that is rated higher that you need, you may get a slightly higher voltage (less sag), just like selecting any power trans.