Thanks Hayzee, good diagram. Yes , that is what I am doing , fitting into an existing opening , taking old windows out down to original framing (2x4`s)and re-installing new with brick mould. The 1/4" and 1/4" (total of 1/2") do need to be subtracted , as well as in my case I am ordering a standard brick mould, which is 1-3/8" (x2). So ,after calling the window store I was told to measure the opening from the outside, (ie

50" width 50" high, subtract 3 1/4" to allow for brick mould , and shimming. So the size of window I would order is 46 3/4" wide ,by 46 3/4 wide . With the brick mould added on by the manufacturer , I end up with my 1/2" allowed for shimming , insulating and caulking.
Replacement windows fitting into the old frame need to be measured inside to inside , in which case capping would be required.
Talk about tricky! I would recommend (not that I`m a pro , just a handyman)anyone getting windows for self-installation to really take their time , check the measurements , and if possible , get someone who is knowledgeable in this area to take the measurements for you and pay if necessary.Once you buy your custom windows , they are non-returnable , and it would be quite a surprise to have a gaping hole in the wall with a nice window that is too big for the opening.
Thanks again, Take care!
Peter