Open the Paint Kit in your graphics editor.
Most all contain layers for detail, weathering, etc. Make sure other layers are below these.
I work by closing all weathering and detail layers leaving only the paint layers shown. Work with the paint layer only, but it is always best to add a new layer above that for your paint. Your individual markings should be in separate layers also.
Just remember the trick is to always work in layers, I have as many as a hundred layers before merging some visible.
Start with something easy, Piglet's models are normally a easy repaint unless he's been eating fermented dog biscuits when he laid out the texture sheets. :d
Caz