Here's my spriting process:
1) Open ROM file in Tile Layer - This may work with other programs, but I
know it works with Tile Layer
Jump to the offset of the image you're editing, and highlight it by right clicking on the first sprite and dragging to the last sprite

2) Export the image to a bmp file

3) Open the bmp in MS Paint. Don't waste your time and effort on a fancy image editing program. Remember, you're editing an image that is, at most, 16 colors, and probably no bigger than 32x32 (unless you're making monsters, but still...). Paint has all the tools you'll need for this process, and won't muddy it up with too many tools you won't need

4) Zoom in as large as possible - 800% for my version of Paint

5)In the Zoom menu, select "Show Grid"


6) Expand your image workspace by clicking on the dot in the center of the lower edge of the image and dragging down. Give yourself lots of room.

7) Arrange the image - by selecting, copying and pasting - into this newly created space.

8) Helpful tip: Create Gridlines around your arranged image so you know the limits of each individual sprite.
Also, create a working palette of all of the colors.
DON'T use any other color, or Tile Layer will not properly interpret it when you're done.

9) Create your new image

10) When you're done, drag the newly created image sprites back into the space from which they originated


11) Then, reduce the image back to it's original size (ckick and drag that same dot)

12) Save your image (no need to "Save As")

13) Back in Tile Layer, import your image


14) Drag the imported image to its desired location

15) Click in the data area, somewhere
other than the imported image, to make the grid reappear over it. this is a necessary step to complete the import.

16) Save your ROM, and voila!

Sounds so easy, doesn't it?
It's not. I'm dreading any and all of this that I'll have to do in the future for my hack, but, well, it's a necessary evil.
Hope that helps!