Just use all your orthographic views, ie: front, top, side, etc... to line up your primitive booleans. You can't do all your modeling from the camera view (or perspective), it's just too hard to precisely align objects without using the flat views. If you want to do a row of negative window cut outs that are all uniform, create the first window to size, then duplicate is (command D on a Mac). Move the duplicate as far away from the first as you like, then replicate it (option D). This duplicate will move the same distance the last one did. Repeat until you are happy or use the multi-replicate feature if you need many more. Using positive, negative and even intersecting booleans you can create some very complex building shapes almost as precisely as you can with any CAD program. Play around and experiment, it's the best way to learn. Good luck.