Pedal to Saddle..setting the Height

When I collected my new Mercian and rode it for the first time, the most noticeable thing was that the saddle was much higher than that to which I am accustomed. And I am not talking mm here.This was the first time that I had ever been measured and specially fitted to gain proper efficiency. It did seem strange, especially as I was also still getting used to the idea of clipless pedals.

The bike is fitted with Shimano SPD  pedals, not that that was a concious choice of mine as I had no idea that there was a choice, but it was the recommendation for a novice.
I have now ridden about 150km on this bike ( it doesn't go out when it is either wet or muddy :-) and am finding that the new position is much more efficient, even more enjoyable. Because of  this I thought I would just check out the saddle heights on my vintage Mercian and my Specialized Hybrid. Neither of these had ever been "set" as I just sat on and pedalled. As such it was not surprising that they were all at different heights, not a few mm but amazingly by up to 12cms lower!  So how do you go about deciding the correct height? And whilst I was at it I also noted that the saddle was not straight on the old bikes, a fact pointed out by Grant at Mercian Cycles.
It seems that there are a number of techniques which can be adopted
a) The Heel Method
b) The 109% Method
c) The Holmes Method

There may well be others. What I have now done is to measure the distance between my pedal axle and the top of the seat on the new Mercian and used that as the correct height; and then adjusted the other bikes to have the same dimension.

The Vincitore Special is proving to be much quicker ( in OAP units ) than I have ridden before and I suspect that setting the correct saddle height is one of the major contributions to this improved efficiency. I am obviously not competitive, but at my age I do need all the technical factors that I can control to be working in my favour. I read that one can lose up to 12% efficiency by having the saddle too low, perhaps now I will be able to ride for longer, I hope so.