As of now i have a 50 gallon reef tank with hang on skimmer and mechanical filtration. On my new setup i was going to use a refugium and didn't know what other type of filtration i should be using.... i don't want to use filteration that will hurt how the refugium will work. The new reef system is going to be 350 gallons including the sump.
Seriously though, can you say some more about your goals for this system? What livestock you plan to keep? Any particular natural environment you seek to simulate?
As a very general response, I would say you'll want a good performing skimmer that's adequate for a system that size, and a means for running GAC and or GFO as needed.
There are lots of options and no one answer covers them all.
What kind of set up are we talking about here a basement sump /refugium with a reef connect to it? or something like a three level system I think I seen someone post up a similar system and it was amazing! All acrylic and a custom stand to match the three tare system. It started as a Reef then frag system then display refuguim then sump on the bottom. I wish I could remember where I saw it on here I'll check to see if I can find the link.
Not to sound rude, but we need more than that to help you. Perfect water quality is a subjective term, and some corals will prefer different conditions from others.
What sort's of corals (or other livestock) are you looking to grow? SPS, LPS, non-photosynthetic, octacorals (soft corals), zoa's/palys, anemones? Focus on a few types, or a garden of all sorts?
Everything has somewhat specific needs. The more different things you hope to keep the more complicated it is likely to be to keep them all happy.
I would like to grow SPS and LPS. This is all being setup in my basement "man cave". So it will be a reef setup with a sump/refugium under it and a couple other tanks that will be hooked into the same system with other corals. The main reef tank will have metal halides and the other tanks will have..... compacts or leds.....