Here's a still frame from my upcoming video called "Watercolor in the Wild," which releases as a DVD and a download on August 11. The whole first section of the video covers materials and methods.
One segment shows how to fill water brushes and fountain pens with the ink colors you want.
I've tried several brands, but none seem as reliable as Niji Water Brushes. I recommend the ones with round tips, but you can also get them with a 12mm Flat Tip. I normally carry between three and five water brushes. One is filled with water, which fills easily under a normal faucet by unscrewing the handle and squeezing the barrel.
The others are filled with blue, black, brown, and gray. I mix the gray myself, put it in an empty bottle, and mark the bottle. To identify which water brush is which, I paint the back end tips with acrylic (see lower left of photo above).
The ink in a brush pen should be water-soluble so that it doesn't clog the brush fibers. I use Higgins Eternal Ink(black), and an old bottle of Sheaffer Skrip Ink. The color in my 30-year-old bottle is mellow blue-black, which I believe is no longer available. The Waterman Fountain Pen Blue Bottled Ink is a bolder blue. For a brown color, I use either the Higgins Sepia Fountain Pen Ink or the Waterman Brown Ink, the latter of which has a redder cast. If you mix two colors of ink, you should mix the same brands.
Several different tools will work for refilling water brushes. My favorite is a Syringe with a Blunt Tip Fill Needle. You can also use a Syringe with a Tapered Plastic Tip (center of photo above). A Glass Eyedropper doesn't always work as well because the tip isn't small enough for getting inside the chamber of an empty fountain pen cartridge or water brush.
I use a relatively inexpensive Waterman Phileas Fine Point Fountain Pen (top) for written notes. In the USA, you can buy refill cartridges in black and blue, but it's not easy to find brown or gray or other colors. As with the water brushes, you can refill them with your favorite color. The pen comes with a piston converter insert, but if you don't have one of those, you can refill empty cartridges with the syringe.
When I need to use waterproof ink for my line work, I like Micron Pens. They come in many colors, and give a constant indelible line, similar to the classic Rapidograph pens. For a brush-style tip, I've used the Pentel Pocket Brush Pen, a waterproof brush-tip pen with replacement cartridges. A caution about the Pentel: the ink can bleed through some thinner paper.