One of the main ways I color and create shadows on RMD.
First, get your sketch drawn out. It can as detailed as you want, but I like to keep it pretty simple, so I can add in all the details as I go. XD
Add another layer, then go over it with the pen tool. I like to make the smoothness around 70-80%, so that the lines look nice and... well, smooth. It doesn't have to be perfect, you can always go over it again.
Once you have the lineart done/nearly done, go ahead and add in the background. (Using a reference can help if you're stuck.) Also, adding the background now helps you make sure you get all the spots for the skin and coloring and such that you might miss otherwise.
Put in all the flat colors, and make sure to keep each color on it's own layer.
Now for the fun part XD. Make a new layer on top of all the others, and put it on Multiply.
Then pick a light color (I used a light purple) and put in some shadows. It's okay for them to go over the edges on the colors a bit, you'll be able to fix that later.
Repeat step 5 on another layer (also on top and on Multiply, and the same color as before), this time going a little smaller in the shaded place.
Then make another layer (again with the multiply, and the same color still) and do it again.
Okay, I forgot to mention this earlier, but MAKE SURE TO SAVE REGULARLY. If your internet likes to crash (like mine does), then your work could get deleted at any time. It isn't fun.
Anyway, so combine those top three layers. Then take the watercolor tool (I call it the blendy tool, but whatever) and make those shadow's sharper edges all smooth 'n' stuff.
Then make a layer at the very top and use the pen to make some white marks where the highlights go. It's okay if they look really blunt, because we're about to fix that: Click the 'Effects' tab at the very top of the screen, then select 'Blur'.
A little box will come up in the middle of the screen, and you can choose the level of blurryness you want. I kept it at 3.
Then go back to the shadow layer and blur that too, if you want.
You can also blur the lineart, but you don't have to.
Then just add some finishing touches. Fix up the lineart, add some flower petals, etc.