As most everyone should know, 3-color potions are easiest to make on Port Royal so go there for all 3-color potions. There is also an alignment method that is Fool Proof.
Here is how to drop your colors (Swashbuckler Stew III used as example). On the Left-most column, drop ALL your Blue/Green combos with Blue to the Left. The green in that combo will occupy the 2nd from Left column. The remaining columns should be Green Green, Red, Red, Blue, Blue. The picture below shows how the fields should look.
Once you have the columns set up as shown above, just drop the colors into the correct column or Right-Click mouse to Flip then drop as needed. The picture below shows both the Green Gators moving to the side.
Since the Green are done, i used the 4th column that was Green to drop more Red. The next picture shows the Red Scorpion on it's way and the potion is done.
For the 3-Color Potions, always use this color order and you will breeze thru the potions. If you need more Red or Blue just use the first two Green Column and add in the color you need in it's proper order.
This method is Fool Proof and makes Potions so easy even a Geezer can do it ;-)