The good thing is that the "rules" for army painting when it comes to sengoku period armies should be seen as more of a general guideline. It's not like Napoleonic armies, and you can find examples of all kinds of ways that armies looked, from those who were almost uniform and well structured towards the end of the period, to some forces that were little more than a bunch of haphazardly equipped troops with very little in common.
Here are the general "rules" as I interpret them after reading a bunch of books (some better than others):
1) Armour were laquered, with black being by far the most common colour. On second place you will find rust-brown, and then red. Far lower than these you will find unusual laquer like blue, gold and green, which were unlikely to be worn by rank-and-file.
2) Dresses were usually not uniform, with samurai typically wearing more expensive and colourful dresses, and ashigaru and peasants wearing everything from barely a loincloth to dresses with more dull colours like brown, grey and buff.
3) Uniforms were rare, and most troops were responsible for getting their own gear, or had them provided by their direct feudal lord. So even if a lord dressed his 25 guys equally, his neighbour would not dress his guys exactly the same. Generally, places with more resources had more opportunities for mass-equipping troops, and you would see more uniformity in equipment and heraldry the later you get in the period.
Units wearing predominately red, for example, are usually from the latter part of the period, when power had started to get centralized around a few leaders. But even the famously "all red" army of Ii, were likely not able to equip their entire army with uniforms, and it was more likely that they could muster front ranks wearing mostly red.
4) Heraldry, in the form of different types of banners, were the main way to identify military formations on the field. Not dresses or armour.
For me, especially at 6mm, these "rules" means that I tend to take some artistic license. If you paint an army with mostly black armour and just random colours for the sleeves and pants, it won't look all that inspiring on the battlefield. Especially not if you have two opposing armies looking more or less similar. So I tend to use coloured armour far more than is realistic, and also semi-uniform dresses.
For example, when I paint my two Takeda contingents, I decided to go with red armour on one, and green on the other. Very unhistorical, but it looks great. For both the red and green armoured ones I paint most of the dresses blue, white or yellow. Also unhistorical, but this means that I get some kind of cohesion between the contingents by using the same palette for the secondary colours.
Most importantly, this means that I get the whole Takeda army to look very different from the opposing army, which has all black armour, with Tokugawa forces wearing mostly blue dresses, and Hosokawa wearing mostly red dresses. Finally, the banners ties the different contingents together.
(Example of varying Takeda banners tieing together the army with uniform colours, despite armour being different. From left: Takeda, Takeda, Hosokawa, Tokugawa, Takeda, Takeda, Takeda)
So, basically I disregard "rule" 2, no uniform dresses, to make the armies look more interesting in 6mm. I find that the scale demands that you paint with strong colours and bold colour schemes, or the minis will just blend into each other. So I might be even more ahistorical in this scale, simple because painting 6mm is a different beast than painting 15mm or 28mm.
As I see it, you can decide to go for representing a historical look as close as you can, or use some artistic license. Personally I use periods with more rigid uniformity (Napoleonics and WW2) to get that aspect of the hobby, and I use less rigid periods (Sengoku Japan, Medieval Europe) to make more "fanciful" armies. As long as you are honest about which way you go, do what suits your passion, and paint according to the end result that you have in mind.
Edit: just because I can't shut up:
When painting Baccus 6mm samurai, I find that I have a limited number of areas to use to convey a colour scheme. These are
1) The armour
2) The pants and sleeves
3) The belt and sun cover on the jingasa helmets of ashigaru
4) The banners
The scale is simply too small and the number of soldiers too large for the lacing on the armour to be a) possible to paint without investing too much time, and b) visible on the finished rank-and-file troops. I do paint them on generals and stuff though.
So, for a 6mm army, I find that if you keep two or three of these areas similar for an entire contingent, you can vary the others and still keep them looking uniform, without looking identical. You will typically want to paint at least one of them in a striking colour, and another one in a contrasting colour that makes the striking colour more visible.
What does this mean? For example, I find that painting the belts and sun cover on the helmets white is a great way to make a dark coloured armour visible. Combine it with a bright colour on the sleeves and pants, and the whole miniature becomes visible, despite them being small. If I went with a dark blue belt, the whole torso and upper legs would risk looking like a blur. With a red armour, you could go with a very light blue or yellow belt, and still get this contrast.
This also affects my choice of colour on banners and sleeves/pants. For example, in the picture you can see that the Hosokawa has a bright yellow banner, black armour, and red pants/sleeves. I find that the two bold colours make a good match, and the black and white areas inbetween them (armour and belt) helps to keep them from "bleeding" into each other.
So, if you are unsure of where to begin with painting 6mm samurai, you could always make a general plan of attack based on these areas. Decide which ones you want uniform and which ones you want to vary (depending on how historical you want to be), and think about if you can put more neutral colours (like black or white) in between the more striking colours.
(Funnily enough, you can basically look at the colour rules for European heraldry for help if you want to avoid bad colour matches! link
