Creatures Caves

With step 1, you've found and copied the base sprites you needed.
Now what?

Important: This method uses with a layer-capable art program.

Cracking a sprite sheet open:
So now that you have your base sprites, you want to mess with the contents, but how?
Programs like sprite builder may have an export option built in, but I find working on 1 sprite at a time tedious. And we're not here for tedium, we're here to have fun and create!

-Open the sprite sheet you want to work on.
-Change the size of the sheet's window until you have nice rows of 4 sprites.
-Take a screen capture of your screen (there's usually a keyboard button for that).
-Open your art program, open a new document, and paste your screen capture in it.

You should now have a nice flat image of a few rows of 4 sprites from your sprite sheet.
Parts like hips and feet can fit the whole sheet in one screencap! Only the long files of the body and head are more difficult.

The blanket:
I've struggled with floating pixels in the past. So many floating pixels, in fact, that I just had to find a way around them, because back tracking to remove invisible blemishes is tedious.
Here's what I do:

Quick Tip:
Layer 1 Black blanket
Layer 2 Colour
Layer 3 Base Sprite

I paste my sprites screencap on the bottom layer (Layer 3), then I use the select tool to select the black around the sprites. The chichi sprites are already clean cut, so copy and paste the blackness on a layer above (Layer 1) and if you make the base layer invisible, you're left with the perfect sprite size with a perfect hole in the middle in the shape of an arm or something.

Then make another layer in between (Layer 2) and colour your new part in, using the base part as reference for lights and shadows.

If you need to change the shape of the hole... well, just do it!
You can use the eraser tool in pencil mode to remove clean cut pixels.
Remove the pixels you don't need and change the hole shape to what your new breed needs!

Exporting:
This part can't really be simplified. To export all the images once they are done, I select the first sprite, copy it, create a new document of the right size, and paste it in. if the document is the right size and i didn't accidentally pick up anything unwanted (like the outside of the sprite) then i use the same selection shape and do the same copy pasting for all the sprites onto the same document. The sprites of a same type in C3/DS are all in the same size of black box which makes things easier.

Once all the sprites are in the proper sized document, I export them one by one as BMP files. Then use sprite builder to import them into the sprite sheet file I'm working on.

Thanks to the blanket method, I've stopped having to struggle and back track due to floating pixels.
It saves me a ton of time and frustration, so I can keep spriting.