Not entirely sure about the limes I'm sure someone else with more experience could give better advice. I do know however that you would only want to use the zest for flavoring as the white rind part will give a bitter flavor.
Use just the zest of the lime, use something like this food grater/zester to just grate off little bits of the lime peel and change the area of the lime your grating when it starts to get to the white rind part.
i have used small ammounts of lemon zest in my beers with good results but search the forums and most people say limes just get too bitter also i have found if you are going to drink the beers green use lots less lemon if its gonna age a couple of months use more