Well I've never used Flux RX so I can't speak for that but I had someone who used it on my showcase thread with varying results.
They're are good instructions on the bottle.
Right now yes manually remove what you can first.
Do some testing and get back to me so we can formulate a game plan I'll help as much as I can.
Test.
Test yourself so you know, and you get good at /understand it.
Try posting this same question on my showcase thread for help. Couple people on there who have first hand knowledge of that product I believe.
Don't worry about putting your hands in your tank. Sometimes you have to get down and dirty with it and nows a good time.
Siphon some water into a bucket, pull out a rock and scrub/pull/scrape in the bucket.
Just be careful of the corals. Might wanna do those in the tank.
Any more questions, you know where to find me.

Trust yourself on testing, not someone else.
Joel