I've tried various methods and this is what works best for me. I use nail varnish, when I can get an appropriate shade (which is most of the time), because it covers more effectively than some paints and is more hard-wearing. I coat the inside of the tube using little sponge-tipped make-up brushes. Buying the nail varnish and make-up brushes has raised a few eyebrows among the staff at my local pharmacy!
The make-up brushes are also an effective way of coating the tubes. Nail varnish applies a thicker coating than paint, so I ream out the hole a bit before applying it if the fit between the tube and the hole isn't loose enough.