Okay, here's an actual example, using the Atlanta Thrashers logo from the GDL 16 ROM. I pulled up the jerseys in NOSE and the logo in TM. Notice that the palette for the jerseys is the same for the logo:
This is why you need to know the home jersey offset to find the palette for the center ice logos. In this case it's "01952334".
So the breakdown of the Atlanta ice logo is a 48 x 32 pixel grid, with each pixel representing one of the colors of that palette:
If you use the palette on the first picture, you will end up with the logo in the first picture. So what happens when you change a color on the jersey? You alter one palette color, but the center ice logo information doesn't change. Just the color:
In this example, I changed the 10th palette color from orange to green. You'll see that every pixel with a #10 changed to that new green color. That's because the CPU is instructed to place the #10 color in this pixel, looks up the color in the palette, and places whatever the #10 color is in the palette in the pixel.
Again, the jerseys and the home ice logo use the same palette. If you notice, the Atlanta logo is only using colors 1,2,6,9,10,15 &16. So any changes to those colors in NOSE will change the logo accordingly. EDIT: A few of those colors you shouldn't edit -- like 01 (transparent/ice), 15 (stick color), etc. for different reasons, but I hope this clears things up about the jersey/home ice logo relationship.