The day I write up a nice detailed guide has turned out to be the day that I am testing a new build of Marine Aquarium Time 2.
With past versions of MAT2, I had been creating logos as Targa files. Targas are big (256kb each) and slow to load (with 20 logos, MAT2 was taking 5-6 seconds to start up). The new build of MAT2 now has full support for the PNG-24 format which resolves both problems!
I tested color, black and white, greyscale, and complex transparency in PNG-24 format and they all work fine. My 21 logos have gone on a diet, from 5.5MB down to 441kb and the startup time is now < 2 seconds.
I'm now re-working the Marine Aquarium Time 2 logo creation guide to cover PNG files....