Yeah, if they are already assembled, that makes things somewhat hard - the access is so bad and the angles are funny, too. That's why it's a good idea to paint the intakes while they are more accessible, that is only partially built up. I had to cut the front parts of the engine nacelles off to fill the seam and paint the intakes right, then glued the painted subassemblies back on.
Hope you can paint your model all right, have a nice day
Paweł