The "Poly->Put Models on Faces" option doesn't have much control over orientation. But if you are matching faces of the same type, you can use "Poly->Augment Polyhedron" instead (or just hit "a"). Start by putting the model to be added in a memory slot ("Edit->Put Model in Memory" or type "m1"), then load the central model, hit "a", and select the memory slot in the top section. Hit OK.
During the augmentation preview, you can use Ctrl+Shift+Left-mouse-drag to move the augmented parts out from the central part, if you want a gap. Then hit Enter when you're happy with the result.
