* "Eye": This is the most common meaning. For example, "I got a wee bit of dust in ma ee" means "I got a little bit of dust in my eye."
* "Yes": This is a more informal, colloquial use of "ee". It's similar to using "Aye" in English. For example, "Are you coming to the pub tonight?" "Ee, I am."
* "And": Sometimes "ee" can be used as a conjunction, like "and", especially in speech. This is less common than the other two meanings.
The exact meaning will be clear from the surrounding context.