Hello and welcome to the site.
Great sticky Romad! You want to decided way in advance if this is going to be a reef tank or a fish only system. Reef tanks are more demanding then a fish only system because it requires better water quality for the corals. Reef systems are also A LOT more $$$ to get running. If you want to start the tank off with just fish and then upgrade to a reef, just make sure you add fish that are reef safe.
A sump is a great thing to have because it increases the water volume which makes it easier to maintian water quality and you don't have to do as many water changes, it also is provides a place to put equipment that you don't want visable in the main display and also can help reduce micro bubbles. A refugium is different, it is more of a refuge for amphipods or other beneficial living things that would get eaten in the main display. Essentially, a refugium is nothing more than a refuge from predation. Sessile inverts and other delicate species need a place to call their own. Isolated, but connected to the main display tank, a refugium allows for common water filtration while at the same time keeping more aggressive fish from impacting it. If you plan on having a mandarin or amphipod eating fish like a dottyback or six line wrasse then a refugium will a be a great place to house their food.
As far as how to do the plumming for everything
I cant help you there lol I am more of a visual person and like to see things in person, if you are the same way I would go to a reputable LFS and have them show you step by step how to set it up
I also know that everyones sump/refugium set up is a little different so it would be good to compare the different set ups and see which one works best for you if you do plan on setting the sump/refugium up.