I use colors off of the rmxp rtp characters so then they don't look so odd.
Then I compare the clothes to the skin shading and try to match the shades closely and determine what shadows over what.
Of course it would be easier if your character is wearing skin tight clothes, but as for this guy's pants I had to reference another sprite.

This hat may need to go though ^ it's a copy of the rmxp captain hat, just with 2 shades of colors and black.
I don't really know how to draw it any different now that I've copied it. :x
Usually referencing other sprites can help.
I also work on Photoshop using layers so it makes it easier to look back and forth.
As an example was this fairy I made by scratch.

I'm not sure if I helped you are not, I don't really know much about art. I'm just really good at mimicking styles.
I still fail at drawing hair regardless. :x
Don't think I'm creative with my sprites or anything. The fairy was based off Chantelise's Chante and RO's Homunculus Lif.
And the pirate guy was based off a character from Gloria Union.