Hi!
its very late at night here in the UK--so this is brief...
have a peek at some of my recent build articles, there are some photos that show the autobodyfiller method as well as the paper--
http://www.modelshipgallery.com/gallery ... index.html
methods that works well for me is this:
In 1/700 scale I use Artists Watercolour paper which has a regular indented texture(try Winsor & Newton); firstly I cut the waterline profile out of the paper 0.5mm larger,this is done by placing the hull on paper and drawing round the hull with a sharp pencil ( before I even think about building the ship) then I stick to the base with either white glue or double sided sticky tape. Build ship to the stage at which you are no longer happy to handle the ship,I usually mount the ship in her sea before put on funnels or masts or photo etch. The ship is placed in the prepared cutout and screwed thru the base so that if it is a resin ship it prevents her warping. I then paint the sea in chosen base colour I add ships wake and bow-wave for (slow speed ) from white/PVA glue and build it up in stages. For medium speed I use Artists Acrylic gel/texture agent and shape it as it is drying. For a ship at high speed I use autobodyfiller for big wake and waves because it sets quickly (30-45 minutes!) so that I can carry on modelling!
In 1/350 scale if the ship is being shown in bigger waves I again use all the above techniques but glue the paper over bits of scrap wood to give the shape of the waves (remember to keep the wood bits clear of where the ship will go....) when the ship is finished ready for varnishing then I paint and drybrush the wakes and bow-waves, this is best left till last as the handling of the base will otherwise make the white go yellow....
I have also used succesfully white toothpaste(!) to really highlight white wavetops etc. cotton wool can be sued but do not use too much or the ship will look as if she is on a cloud....