If you split it up, try to get all pieces roughly the same color. Then knead them all together, 1 piece at a time.
For example, if I had 1 kg fondant, I'd split it into 3 equal pieces. I'd color and knead each piece separately to roughly the desired color. Then I'd combine 2 of the pieces together and knead until all the color was smooth and even. Then I'd add the last piece and repeat.