Both, but you should should FF for new scripts and such, because 00 is also registered in the rom as other things, such as a space for example if you've ever hex edited text, while FF is nothing.
If you are using ntme and inserting everything correctly, try using free space that is below 800000, so basically uncheck search from offset 800000 and use from beggining, then use offsets from there. I had the problem too, and I just used those and it worked :P
if by rearrange, you mean edit them, then just open up the color picker in ape, put in your rbg color code andat the bottom of the color picker somewhere you'll see the GBA color code that it gave you, then you just put that in the game using ape, if you don't know how to use ape, find a tut on it