So, here is some info on how I render things now :U (Though like how I do everything is subject to change). Also, I use Manga Studio 5 EX/Pro version so you may not be able to re-create this depending on what software you use.

(See image captions so you know which layer I’m talking about down here).

1. After making the lineart. I create two more layers. These are ‘shadow’ (img.1) and ‘flat’ (img.4).
2. On the ‘shadow’ layer I select all the colors around the character and then fill it with 50% grey.
   
1. It HAS to be 50% grey for this to work.
   
3. On the ‘flat’ layer I color the character in. Then I set this layer to Overlay.
   
4. After all that I color in the shadows & highlights on the ‘shadow’ layer.
1. For the shadow color any level of 60% grey - Black will work. Pick whatever suits your preference.
   
2. I got the color I use by taking 50% grey and using a Multiply layer over the base to get the color then merging them together.
   
5. Once all the shadows are done I start creating Gradient Maps (GMAP) (Layer > New Correction Layer > Gradient Map).
   
1. To create the GMAP I use:
1. Create a color point in the center set to 50% grey.
   
2. Now using either the default black color point or a new one set that to a different color. This color needs to be dark and  somewhat desaturated to work. You’ll need to fiddle around with it till you find what works for you.
   
3. You can use img.3 as a reference to get an idea what colors to pick.
   
4. You’ll need to fiddle with the position of the color point to get the color exactly how you want. Just eyeball it.
   
2. This part is a little tricky because it’s ultimately up to you how many you use it’s just important to remember the GMAP will only control the shadow color not the “base” color as seen in img.3. For this picture I only used 4 GMAPs (Hair, Skin, White, and Brown). 

Hope this is helpful or at least interesting.