Traditionally all incoming lines into a server room or wiring closet gets punched down to a panel in the rack and then jumpers are wired to everything in the rack. You never put an end on a cable that came out of a wall. The idea being you would have maybe 5 feet of extra cable in a loop behind the rack in case you needed to reorganize the room in the future. It sucks pulling cable, so leave some extra.
If there were multiple racks then usually one of them was just for wires and switches and the others were for servers. I usually used different color cables for different things too (like use orange for links between switches and blue for servers, etc), but for a home rack I wouldn't bother with that. Different color zip ties on cables can be handy too.