I painted several boxcars with a brush and in my opinion they turned out well. Especially if you are going to weather them... brushing them with the faded colors you want anyway is the way to go. My thinking is, why strive for a "factory-perfect" coat of paint when you are just going to fade it and dirty it up and rust it up anyway?
I brushed on some thinned water-base gray craft paint as an undercoat, and then put on three or four layers of thinned final color craft paint. I also made each layer a slightly different shade by mixing in grays or variations on the color. By using several coats of thinned paint, you can avoid the brush marks. Another plus is there will be some moderate variations of color on the car, which is a good start on weathering.
As for decals with white lettering, Ralph is right on. Print the background with as close a color match as you can get to the body of the car. Cut the decals following the letters... there will still be a little of the color showing. Then, once the decals are on the car and micro-sol-ed and dried for a day or so, you can take your paint and blend over the decal border so it matches the car. You may also have to take some white paint and go over the white letters a bit, as they are a tad translucent. None of this needs to be perfect if you are doing a weathered car. Once this is done, give a couple of light coats of dulcoat which will help hide the edges of the decals.
This worked for me, give it a try!
