i think a lot a people paint small items on the sprue and then touch up the area when the cut it off. i suppose it's personal preference.
As i usually do vehicles i tend to glue all the bits (large and small) together in sub-assemblies then paint the whole lot the base colour then pick out details after, this works for me.
Never built a passenger aircraft so i don't know what parts there are, i would imagine the the cockpit and passenger seating can be made up seperately and painted before encasing it in the main fuselage, this would help you to do any detailing on these bits beforehand.
As far as painting goes, I would brush paint the internal bits and then (when the planes put together) mask off windows etc then spray paint the exterior to achieve a nice gloss finish.
Like i say ... i dont do planes so there's someone out there (such as Ian ^above^)with a lot more knowledge and experience to give you hints and tips.