Can you lower the soft top on a jeep without taking the windows out?
No, you will have to cut down the the windows therefor you will break them.
How do I fold down the top of my 1994 jeep wrangler yj sport wg without removing it to store on the vehicle in a top storageboot i know i have to remove the windows first?
It depends on if you have a factory soft top or after market (like Bestop). But they should be similar- remove the side & rear windows, then remove the canvas top & fold the frame. If it is factory, look for an owner's manual for your Jeep or look on manufacture's website for directions. I was able to download a user's manual for my Bestop from their site.