You can go either way; you can just basecoat then do the lines then do the panel colors, though then if you screw up panel colors and have to re-spray the base coat, you'll have to re-line nearby panel lines.
If you do all the colors, you might be a little safer, since pencil will erase if you screw up the panel lines.
Honestly, it's just a matter of preference. If you want to break up the job a bit for variety's sake, do some lines, then paint the panels, then finish the lines. Whatever makes sense to you.
At any rate, get all that other stuff done then decal the model LAST, after a good, shiny gloss clear coat. Then you can spray a matte coat (Testors has Dullcote spray in a can that's available widely). The trick with those clear coats is don't go too thick. If you use lacquer-based clear coats, they can yellow with age, so go somewhat sparingly to reduce that yellowing on down the road.