the color changing on your substrate is normal its your first alge bloom. a salt tank will go through several of these this is the process of the tank maturing. after 6 months or so the worse of maturing is over but it take a tank a full year to fully mature. what you have is a brown diatom alge its usually one of the first alge blooms a tank gets.you'll probably get hair brown,green, or both. plus many others
i would try to change the cc over to ls before the tank gets to established. to go cheaper you can get dry sand and seed it with some ls from somebody elses tank or a lfs. also when if you pull out the cc it would be a good idea to take the ugf out. 1. they dont work well with ls 2. ugfs with cc become major nitrate factorys. also with lr it is better with reef or fish, lr and ls will become your main filters for the tank.
go with fo so you can learn the basics of salt then after the tank ages a little you can think about going with corals. its a lot easier to switch with ls and lr already in the tank.