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While it may seem odd, a common use with gundam markers is to press the pen tip into a tray to extrude paint, and then use a brush to apply the paint. I say it seems odd cause normally you’d just think “it’s a marker filled with paint, so why use a brush?”, but if you want to get into those tight spaces, or not mess up painting small parts, you can use that method to do so. Using it as a marker itself is best reserved for going over large areas.

Acrylics and enamels are the most common sorts of paint to hand brush on plastic models. Though acrylic is the most common these days, it has some flaws to it. The biggest is that it is not as durable and strong, but safer in use.
Enamels are really strong and almost scratch resistance. The drawback is that they take a much longer time to dry. Acrylics are dry within hours after application, as enamels can take a day or two. Both depending on the thickness brushed on.
There are lots of techniques in applying paint. It depends on what you intend to do with them. On a large surface, diluting the paint and brushing on several thin coats is the way to avoid brush strokes.
When painting raised parts on the surface of an object, holding the brush at an angle of 30 percent and then brushing from the middle outwards to the edges will prevent hitting lower parts.
When filling in indentations, or tight spots, diluting the paint to a consistency of milk, load up the brush with paint will make it flow in crevasse and towards edges. This method is also use for panel lining. If the base paint is covered in a clear coat, all the excess paint can be taken of with a cotton swap dipped in the same solution which is used to dilute the paint.
For diluting paints, there are several options for both acrylics and enamels.
Enamels; lighter fluid, white spirit, benzine or an expensive enamel thinner.
Acrylics (water based, like Valleo); water, ammonia, demineralized water or a purposed thinner
Acrylics (alcohol based, like Tamiya); Isopropanol alcohol (at least 91 percent) or a again expensive acrylic thinner like Tamiya X20
Whatever you do, never use a cellulose thinner. This will eat trough all the layers of paint, and even trough the plastic.
Should you choose to use a acrylic based paint and want to seal it of with a clear coat from like say Tamiya in a spray can, the first layer should be a really fine mist and at a distance of at least 30 centimeter or 15 inches. Spray cans are mostly lacquer based, and these can eat trough acrylics, even trough enamels to some degree.
From weakest to strongest paints; Acrylic water based, Acrylic alcohol based, Enamels, Lacquers.
It is no problem to use a weaker paint on top of a stronger paint, the other way around can cause trouble.
As for brushes, a good (expensive) brush is better then a cheap one. Depending on what you wish to paint, get several thicknesses. If a brush is a good one can be fairly easy tested. Make the brush wet with water. “Paint” a figure of 8 on you hand. If it is a good brush, the fiber or hairs on the brush will all come back together in the same shape as the were. Never store them on the bristles and wash the after every use. For storage you can dip the in some vegetable oil to keep them moist for a long period of time.
This is all I can think of right now, but I’m sure I left some things out. Please give a shout if you need some more clarification or information.