You should turn your windage on the scope all the way from one extreme to the other, and count the clicks. Then you center the scope's windage. After mounting the scope, use the windage on the base to get your left to right adjustment about perfect. Use the scope windage for the remaining adjustment. This assures that the plane of the lenses in the scope are nearly straight with each other, rather than cranked to some extreme angles. In theory, the sight picture should be better. For certain you will have the same amount of left and right adjustment should you ever need it.
Those windage adjustments on the base are not as crude as you think. You can get the scope almost perfect by just using those screws simply by bore sighting down the barrel.