Keep your stem flipped up while gradually lowering the stem by moving spacers from below it to above it. When you've lowered your flipped up stem to the point where the saddle-to-bar drop is the same as it would be if you flipped your stem and moved a few spacers below it, then you can "flip it" and be in pretty much the same position you've already gotten used to.

Personally, I did it all using basic geometry to figure out how many spacers I'd have to move to make it all equivalent. If math isn't your thing, trial and error (while using a ruler) will work, it will just take longer.