I am going to work with the idea that you have an airbrush, so if you don't, then just change this to meet your methods.
after you wash the parts, and rinse with Cold water, let the parts dry.
Mask off the canopy on each plane, then paint the plane overall in the interior color. After that dries, paint the plane in the bottom gray, let dry, then paint the plane in the top gray. If you have any trim colors, mask and spray those.
then remove the masking on the canopy, and you have the interior color showing through the clear, just as if you had painted the interior separately
if you try to do a "patchwork" of the interior color, that patchwork is what will show through the clear canopy bump, so don't shortcut that part
Rex