Short answer is yes. As I explained before, it doesn't look at what you've placed in the statics by hand. It places based on the last run of Dragon.
So if you answer no to "Clear Statics?" then yes, it will most likely cover them. If you answer yes, then it will wipe anything you've placed by hand.
As an example, if you have forests in the map, and you manually put a dirt path (or anything) in the statics in that forest, then when you run DragonSP, it may put tress on top of your statics. Keep in mind it's random, but don't count on that to save you.
-Ryandor
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