Normally, even on 1/48's, I do the same thing as Paul. In fact, it's the easiest method I know to replicate the interior frame colors in canopies (insides are mostly molded flat and devoid of detail anyway). For larger scales though, I would imagine some kits come with the frame detail also molded inside the canopies. Maybe for a perfectionist the aforementioned trick simply wouldn't do, as it would not give the correct illusion of depth specially when the canopy is opened. Though I haven't tried this yet, I think the easiest way to mask the canopy interior would be to re-use the same masks (assuming you use tape) used for the exterior. You may have to "flip" some tape "panes" since the sticky side will now be facing outwards. You may also have to trim the mask a little to fit on concave sections. Basically, you'll just be using as much of the exterior masks to do your interior to save on cutting new masks.
By the way, what project do you intend to tackle (or are tackling now)?