I’m not sure what you mean by both sets. The code phrase comprises 3 words that read from left to right from the start of the 5 x 5 letter square, as set out in the example in the instructions. The pattern is not 4,4,6. If you’ve solved all the puzzle, you will have a whole series of pairs of letters and their coded counterparts. If you go through them systematically, you should be able to work out which of these pairs of letters fall within the same rows or columns, though you will need to work out the correct order of the letters.
I hope that helps.