Welcome. Not sure about that table and not too sure what you mean by a setting to make the router flush with the table. Would you mind posting the model numbers of the router and the table.
The router is normally hung from the underside of either the table or, preferably, to the underside of a plate. So the router is usually below the top surface. Plates are generally 3/8ths of an inch thick. If your table doesn't have any sort of plate, then it will likely have some kind of clamp to hold onto the router base. At any rate, you will be moving the router bit up or down. Depending on the bit, thickness of the work piece, even whether you use a jig to set the height, you will set the height to whatever produces the cut you want.
I hope Stick will post his collection of pdfs on using the router soon. You want to read and understand what's in them BEFORE you start using the machine. Improperly used a router can cause a lot of damage. Using it in a table is far safer than freehand operation. Looking forward to seeing what you're making once you get it in operation.
The more I do, the less I accomplish.