Assuming these are the reddish/brown flatworms, because those are the only flatworms Flatworm Exit will kill, not the acropora eating ones. That said, I've used it myself a few times, and yeah siphon out as many as you can, what I did was use a hose with a fine mesh sock (not felt) tied to the bottom in the sump, then I could spend as much time as possible siphoning out as many as possible. Do this when your lights are all on their brightest since those guys are photosynthetic and love the light, so it'll be easiest to pull them out. Try to get every single one you can see to reduce the total amount in the tank. Then when you dose your FWE, I'd probably dose 25% more than what is recommended, empty your mesh sock contraption and be ready to siphon ones that pop up in the water column, one thing I noticed is that many had a stringy attachment to rocks so they kind of floated up. Depending upon how red your water changes would dictate how much of a water change you might need, or more to the point how soon you should do it. You can always pour tank water into a white bucket and look at the bottom to gauge how "unclear" the water is, do your big WC, if you have a 20g frag tank I'd do a 10g WC at a minimum, but add the carbon after so that it doesn't get saturated as quickly, let that run and you should be fine. Repeat the procedure in a week to get any stragglers that might still be around, and it probably wouldn't hurt to keep the lights off for a few days so any flatworms that are still around don't regenerate via photosythesis (your corals will be fine.
There really is no reason pull corals out and dip them though, if anything the toxins will be worse off for fish than for the corals.