You really need to do the smoothing first and the doors ect have to be cot out of the smoothed final shape otherwise it will be difficult to blend it all in afterwards

Garry
I too second this, and also take it from our...well least mine...not sure if garry makes models (I assume he does) its better to smooth every thing on the model, then do the cutting out/animation of parts (when it comes to things like doors, windows, etc on the physical plane fuselage its self) then to cut then smooth...I seen people in my college cut then smooth with very disastrous results (granted they wernt working on a plane but still they had some pretty complex models)
and if posible, if your gonna add shine to the windows them selves and all have the windows on there own texture so that way if you want to tint the windows a bit you can, also PLEASE PLEASE PLEASE take your time and continue to do what your doing, listening to feed back of others is one of the best if not the best way to take your model from ok to "HOLY $NIT I MUST HAVE IT NOW NO MATTER WHAT" type of plane...(well you get the idea at least right?
point is listening to the feed back of thoes who are testing/working on the project with you is the best way to improve and it also offeres the advantage of having multiple sets of eyes to help catch small little erros that someone or you may have missed.
example I didnt notice the hairline crack in one of the windows, but I may wind up finding something else that was compleatly overlooked or thought to be "normal" which I do have a sugestion for the left wing.
when the wings are open (setting one or more) I can see bits and pieces of the wing piece through the fuselage (hard to describe) bast way to see what im talking about have the main body one color (say black) and the wings white or some other bright color and that should give ou an idea of what I am talkin about...link to picture coming shortly (or by PM if needed)