What is your substrate? is your substrate conducting then you have to support it on a thick metal desc such that the current is forced to be distributed uniformly at the whole surface of the substrate. The other precaution is to mask the areas free of gold by an adhesive tape or photoresist film shaped by photo lithography.
The third precaution is to make the counter electrode area eqaul to the working electrode area and finally you have to stir the solution to homogenize it.
You may use; seed layer at first, than pattern via lithography (desired area should be open), Au EP deposit. then you can remove seed layer by a proper way (wet etch or dry etch with the use of photolithography)