Its more or less the same as painting the rest of the kit, but more sanding is required. Bandai machines these parts to move perfectly as they, adding paint will hinder the movement, so sand beforehand and keep in-mind the following:
- knee/elbow joints: http://dalong.net/review/mg/m55/p/m55_m0006.JPG. Take a look at how the elbow joint joins with the arm armour plates. The elbow joint's female connector will bee too small for the armour's male connector and will cause stiff movement. Same thing will happen to the knees and anywhere else similar assembly is needed. So again, sand.
- female/male connectors: During painting, if you get paint in/on these areas, assembly will be a right pain in the arse as the parts will be very difficult to snap together. To avoid this (since you cant sand these) either cute the male parts in half or all togather and use glue during assembly, or gouge out the female parts with your hobby knife to make the holes bigger. I do the latter since its quicker and no need for glue in the end.
What i do personally is make all the internal parts at one time and then paint them. At the moment i just finished painting all the assembled internal parts for MG S Gundam (so completed steps like Step 1 in the above link) and then the parts that are stand-alone like K5 in the link. It depends on you too. I only painted the parts i knew were going to be visible since i dont care much for displaying my MGs without armour.