You don't must use the predefined layout. You can set all manually. See
example in the "gnuplot help":
set multiplot
set size 0.4,0.4
set origin 0.1,0.1
plot sin(x)
set size 0.2,0.2
set origin 0.5,0.5
plot cos(x)
unset multiplot
I think than works the margins also.
Jörg