Dingwall
I know there is no right way as such but curious to know what you guys do.
I personally run : Guitar --> low gain pedals --> higher gain pedals - end with boost --> amp (I do use other pedals too but this question is aimed at gain pedals)
(this was based on reading stuff and have not really tried running them the other way)
Gearhead
High gain has a tendency to compress your playing. If you then add low gain, everything becomes lifelessly allthesame. With your order of pedals, you can at least try to keep some dynamics.
AlanRatcliffe
It really depends on the particular combo of pedals and your taste. You have to experiment to get the best out of any setup.
At the moment my setup is low gain into low gain - both very good at retaining dynamics. The first drive (Barber LTD) is setup to give a slight volume boost and add a bit of treble. The second (Lovepedal Amp Eleven) is set at unity gain and with a completely transparent EQ. That way I have three distinct, usable drive sounds: slightly dirty, slightly dirty with a slight volume and EQ boost for low gain soloing and both together give me a nice, thick medium gain solo tone that can still clean up nicely with volume control and/or softer playing.
The nice thing with my current setup is the drive tones all sound like extensions of my clean tone - like a good dirty amp that cleans up real well. I also don't have to change anything for different guitars - each just brings it's own tone/output level to the table.