When you add a sump to an existing system, it is more or less a DIY project. There really is no one best way to do this because a lot depends upon what you want out of the sump and how large it is. In short, to a large extent, you are more or less on your own.
There are a number of correct ways to plumb a sump, depending upon what you want to do with it. I suggest you look at sump designs not only for the system you have but for reef systems in general. Learn what sumps can and can not do for you, and figure out the options you want in your sump.
What you do with the existing filtration system depends on what you want to include in your sump design. Since the system is fairly decent out of the box, I suggest you only include functions in your sump that you don't have or you consider inadequate in the standard design.
Your going to find out that for items like this there are not too many hard fast rules. There are some considerations to take into account. Like many things choosing one way of doing things may limit other things in the design.
I'll give one example. When you plumb something like this you can choose between clear plastic PVC hose and hose barb fittings or more traditional PVC pipe and fittings. Clear plastic hose is easy to install but those hose barb fittings restrict flow. PVC pipe will give much better flow, but is a lot harder to install and all the joints must be glued. This is a bit of oversimplification and you can use both methods at different points, but it makes the point about the design.
I suggest that you figure out what you want the sump to do, and how you want to set up and plumb it. Then post the design here, and let others offer suggestions and comments about it.