Now, it really depends on the type of paint you're going to be using. I always use acrylics, but sometimes I go with the more expensive Testors paint if I feel a custom doesn't need much weathering. For this first custom, I didn't do any weathering whatsoever. I just used Testors paint for the yellow parts, and some cheap acrylic brown paint for some very subtle work (the chest straps and a few lines painted in the folds of the clothes).
First, I assemble the parts... for example, I wanted to make an Ithorian citizen recently, that required a bit of painting.
head - SAGA2 Hammerhead
scarf - SAGA2 Hammerhead
torso - Legacy Zuckuss
arms - Legacy Zuckuss/SAGA2 Hammerhead
belt - Legacy Zuckuss
skirt - SAGA2 Kitik Keed'kak
legs - SAGA2 Hammerhead
The Testors paint, I just painted in thin layers on the clothing area. Then after it dried, another coat, and finally I toughed up with the brown paint. I didn't paint the skin at all, here's the end result:
Now, there are also times when I rely mostly on the cheaper acrylic paints, like Apple Barrel and Delta Ceramcoat. When using those, it's usually because I know I'm going to be doing some washes with the figure to bring out more weathering.
Here's one where I wanted to do a bit more weathering on, which is a Rodian. Here's the parts used:
head - POTF2 Greedo
torso - Comic Pack Tol Skor
shoulder pads - Comic Pack Tol Skor
biceps - Comic Pack Tol Skor
forearms - ROTS Clone Trooper
hands - VOTC Greedo
belt - random fodder
thighs - Comic Pack Tol Skor
shins - VOTC Biker Scout
On this figure, I did the following:
1 - Prime the areas I want to paint - basically everything except the head and hands. I took black acrylic paint, watered it down just a bit, then painted everything in a thin layer. Let it dry and did it a gain.
2 - Using the different colors now like the green you see on his thighs, I mixed in just a touch of water to make it apply smoother. Paint lightly. Let it dry, and repeat 1-2 more coats.
3 - Now paint the other areas of the body using the same method.
4 - After it's dry, try a method called dry brushing - getting just a touch of paint on a wider brush, and brushing most of the paint off. Then brush the brush hard over the figure, the details of the sculpt will emerge - on this one I dry brushed most of the areas on the armor (shins, forearms, chest) with an off white color.
5 - Allow to dry for about an hour. Now mix some black paint with water (90% water) and brush it over the freshly painted areas. Allow to dry. The wash here will soak detail into the custom. Allow it do try.
6 - At this point, there are areas like the thighs where I did another dry brush, back to the original green color of the thighs. So what you have on the thighs is a black base coat, a green coat, a black wash, then a green dry brush. Lots of time, but gives a nice effect to add depth to it.
7 - Fine detail areas like the chest, since I dry brushed the off white, that's why you see the rectangle outlines colored. What I did to fine tune it was repaint the inner parts of the rectangles with the blue color you see. That's a lot easier than painting those thin little lines.
8 - Other areas with the shin pads, where you see multiple colors, it's just a matter of using thin brushes to paint it. I usually do areas like that last.
9 - After it's dry (since I did NOT use Testors paint on this one), I spray down with Matte Acrylic Sealer Spray from Walmart. It comes in a blue bottle like spray paint. Spray 2-3 coats on the figure, but not too close to it. Allow to try.
Now, there are also times when I need to work out an issue with joints. My suggestion is to try to avoid painting them if you can, because we all run into problems of joints chipping. So, look at the joint and determine if when you move the joint back and forth, if the plastic rubs at all. If it does, you already know that if you don't take some preparations, the paint is going to chip off.
So, what can you do about this? There's a few options...
1) Don't paint the actual joint.
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2) After you paint the joint, use super glue (liquid kind) and glue the joint, but only the part where paint would rub. Essentially you still have some articulation, just not ball-joint quality. But it will keep the paint on (after the glue dries, paint over the glue).
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3) Trim the plastic around the joint with and exacto knife (so the joint doesn't rub), and then paint.
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4) Sand down the actual joint itself, then paint.
I usually go with option (3).
In doing so, after I trim around the plastic, and try to smooth out the areas that I trimmed, I paint the joint. After painting, I take a toothpick and apply liquid super glue over the areas that would rub if the joint had not been trimmed, but I'm careful to not let the glue leak to areas where it would restrict articulation. After the glue dries, I repaint over those areas in an attempt to make it look seemless and natural (this is also a good practice when repainting palms of hands of figures due to holding weapons making the paint chip). Also, make sure you are painting in VERY thin layers.
Hope that helps some!