First remember the models in most estes catalogs were never flown! some were but very few.
That said:
The easiest way is to paint only the bottim of the cone and top of the Transition, mask off the open center and paint the esterior of the plastic payload section at the same time as the body,nose.etc
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Or fill, sand and paint your Transition and Nosecone as you like. if your Clear section is anything like the ones I've used over the years it will be either Toooo tight or way to loose. If to tight not problem, sand to fit then repaint and assemble with a clear watch crystal cement on the transition ONLY! the Nose cone is ment to be removable. Taped to the exterior of the model during flight. I use 1/2" silver mylar tape for this, Looks good in the air and doesn't tear up the nosecone finish to much when removed.
If the clear is too loose, you'll have to build up the transition and shoulder with masking tape, fill sand and paint then fit the piece attached with clear drying watch crystal cement or something similar. If your unable to find a suitable adhesive, and the friction fit is good I'd suggest a second coat of wet paint squeeze on the payload tube and let dry, to not twist, turn or otherwise disturb the tube during this process, I have had model payload section adheared in this way were the paint/friction fit has been tougher then the clear polyethylene tube itself.
I'm not sure if you'll be able to see my constellation in this group shot from back in the day but it's the 3rd model on the right Orange and red. I try Never to paint my models like the package unless it's a scale model
Hope this helps.