Since you're beuilding a ship, and I am assuming you don't have an airbrush... I think I would go the spray can route if you can find the color you are wanting.... I'd spray all the decks, hull and superstructure right on the sprue. If it is a two piece hull you'll need to repaint the bottom anyway so it wont hurt to sand the grey when you get the seams out... if it is one piece better yet!! just paint OVER the grey when painting the below waterline color...
Once it is all finished and hull seam sanded, just hit it with the spray again to cover the sanding and putty you did, maybe a light coat over all the superstructure/deck areas and WAALAA!
As far as below the waterline you could go brush or can on that... I think I'd spray the main (under the waterline) color and mask and brush the demarcation line...
When it is all done, I would use something like Testors dull coat (after decals) to make it one even dull look...
Since you said you are a beginner there is a good how-to page on Swanny's website on how to fill gaps in a seam with putty and get it looking good... here it is:
http://www.swannysmodels.com/Seams.html Almost every two piece hull I've built needed a little putty at least...
hope this is a good build for ya! maybe you can post the pics of it when you're done so we can check it out!