Well if you have extensions that will help clean up the FP code, then i think it'll be fine if you use that method. It might be an idea though to perhaps test those extensions on a dummy page first to be sure they'll work decently. I think DW will tell you though upon installation whether an extension is compatible or not. So you won't have to watse your time testing.
However, still be prepared to have to do a wee bit'o cleanup afterword. After all... nothing is full-proof i'm sure you know.
That's about all you can really do for this i think Lily. Otherwise, what else might one do to prepare? Not much i would think.
I would think that so long as after the conversion, your pages still look right visually, you've been successful. That for me would be about the only telltail sign.