I am not sure what dipping material you are using here. I can only speak of experience using the Army Painter "Dips" . To prevent pooling I go around the models after they have been left standing for about 10 minutes with another brush dampened with brush cleaner or thinners and remove any pooling I don't like.As regards brushes I use those cheap nylon bristled brushes available from stationery stores. With the use of Revell Brush Cleaner they clean up really well.As regards the colours to use. For the Confederates I would use strong tone .For the Union ,Army Painter recommend the use of the Dark tone ( black pigmented) for blue uniforms. I have used it with success on my Portuguese Naps which are also blue and look really good.