At one point it seemed like the facial spray apps were done in two parts because of this:
(This was lovingly named the Abraham Lincoln Ben variant
)
But apparently that would have been far too costly and time consuming so the paint mask for Ben would have been a single piece that did the entire head (hair and beard), the figure above is probably the result of a faulty mask and isn't enough evidence to prove that two masks were used but it's still pretty cool.
EDIT- went off on a bit of a tangent as I didn't read your question properly! But yes any paint app that required a different colour had its own mask, the eyes were done using a different mask to the hair because they are a different colour.