Hi jsapair,
This is how I did it. FIRST, deactivate (un-check) your RTMM scenery in FSX scenery library. Press OK to rebuild the scenery.cfg file. Close FSX. Then make the directory changes, moving your folders from "addon scenery" to the Misty Moorings folder. Then restart FSX and open your scenery library. Select the first deactivated RTMM folder entry and click on "EDIT". When the window opens, the scenery name will be "highlighted". COPY it by pressing Ctrl+C. Navigate to the new location and left click on the corresponding folder. You'll notice there is nothing in the scenery title box. Click in it and paste the name you copied previously in there by pressing Ctrl+V. Click OK, and left or right click in the next window. Put a check in it's box to activate it, and go to the next folder. Do that for each scenery location, to change it's path. I did it last weekend, and it was 141 folders. You're lucky if you've only got two installed so far.