Taking the
UGF out may give you the opportunity to really get the substrate clean being that UGFs are extremely messy. Get all that gunk out if any that has accumilated while the
UGF was in operation. That's what I would do. Then I'd add about two inches of new substrate. The lack of oxygen in the bottom layers will create de nitrifying bacteria and naturally help control nitrates. Certain worms, snails, starfish and fish that live in the sandbed will release any build up of hydrogen gases that can become toxic. Some people don't like the idea of constructing a
DSB, but I find it useful and provides a natural means of keeping nitrates under control. With all that rock work you'll have, vacuuming the substrate is next to impossible. The de nitrifying bacteria will break down nitrates without the need for vacuuming. It does it for you!! I think that's a beautiful thing in this back breaking hobby.
LOL. You still need to exchange water. Nothing can replace the need to renew some of the water periodically.
Having a protein skimmer and live rock, you shouldn't need any additional filtration, so the internal can come out. It'll only take up space you'll want to use to display a nice piece of coral. You also don't want to keep carbon in the system all the time. Use reef grade carbon for a week each month.
It's good to put in live rock when there is no toxic ammonia or nitrite to start with. It may create it's own ammonia shortly after for a brief period. So long as it's not going into a tank with present toxins, it's ok to add live rock. Things can acclimate to slow rising levels of toxins, but cannot acclimate to sudden exposure to toxins. Though any nitrifying bacteria on the rock may or may not be affected, there certainly would be other microbes that make up the water chemistry that would be affected and can extend the time it takes to establish the nitrogen cycle.
Don't fill the tank up with live rock right away. Take your time. My first reef, that was my mistake. I had so much rock work going in there before anything, by the time the tank was ready for coral, I had no room for the rocks they came on...lol. Luckily I work at my
LFS and was able to take some rock back. It's perfectly fine to use live rock to seed base rock. Eventually it'll all look the same with nice natural growth as the system matures.
A system started with live rock varies in the time it takes a system to become established with nitrifying bacteria. Some systems take a week or two, others may take a month or more. It depends on the amount of decaying debris on the rock as well as any other waste factors. The more ammonia produced in a smaller amount of time, the longer the establishment will take to complete. You always want to take your time when populating an aquatic environment so the animals can adapt and the system can adjust to each new waste level that comes with every new animal that enters the system. Fish produce much more waste than inverts, so this applies more strongly to fish. You can pack a tank with coral, reef crabs, and small snails and shrimp without barely making a dent in the waste load. It's the fish that you want to really take your time with.
Once established, the nitrifying bacteria will only have enough of a population to maintain the current waste load. One to two size appropriate fish at a time is ideal and a week or two in between introductions will allow the bio to catch up with the new waste levels. It also helps the new fish by giving them time to adapt to their new surroundings.
If you have any other questions, by all means do ask. The biggest mistake people can make in this hobby is not ask questions. When in any doubt, ask and always read. Arm yourself with knowledge. It make a difference between a flourishing system and one about to crash. It doesn't take a lot to maintain a reef, but it also doesn't take a lot to kill it too. So even if the questions seem silly or too numerous, they are not. No such thing in this hobby.
