Boggle - Letter distribution and face orientation of each die
I believe you'll find that the answer doesn't matter for your specific case:

If we assume every die is a fair die (which means every face has exactly 1/6 chance of coming face up, and is what you should strive for when building the cubes for your version of the game), the position of the letters in each die will not matter, since every face will have the same chance of showing up in your grid, and each die can only ever show a single face. 

Therefore, all that matters is the distribution of these letters, which will ultimately affect how many instances of a letter you'll see in your board; and you seem to have found a pretty solid distribution for the standard English language scrabble.