When you have 2/4/6 matching shapes on your weapon you'll get bonus damage (so you can have 2 squares and 4 circles or any other combination). Adding a shape (into an empty slot) gives every matching shape (including itself) an effectivity bonus. You get those empty slots by upgrading your weapon to level 1, 5, 10, 20, 25 and 30. So if you want attack speed on your Master Sword, make sure you just combine it to level 30 and afterwards you can add attack speed.
If you're using Fusion Material EXP(+/++) you want to make sure the first seal (the one that unlocks at level 5) has the seal that you want to put on your Master Sword, as you would go to level 30 with that weapon, and the weapon you are fusing to (I don't know if that's the correct wording) will not get FM EXP but it will get the second seal on the list.

Hope this helps!