I have two TGraphAsymmErrors (of distinct colours), and have them on the same plot using TMultiGraph with the drawing option “A4”. The goal is to have two uncertainty bands of different colours with some transparency so that their overlaps can be clearly seen. I have mainly tried using h->SetFillColorAlpha(kRed, 0.5) but this makes no difference whatsoever. I know that there might be a way to do this using TPad transparancy, but my plots are already on some TPads, so this might make things a bit too crowded.
I once had a similar problem.
In the end I solved it by assigning the fill style 3345 (diagonal lines from top left to bottom right) to the one area and the fill style 3354 (diagonal lines from top right to bottom left) to the other one. If the fill colors are different, the overlap region is optically good visible. You can also try to play with the distance of the lines in the fill style (varying the second number - 3145, 3245, 3345 … 3945)
" The transparency is available on all platforms when the flag OpenGL.CanvasPreferGL is set to 1 in $ROOTSYS/etc/system.rootrc , or on Mac with the Cocoa backend. On the file output it is visible with PDF, PNG, Gif, JPEG, SVG … but not PostScript."