Most rearsets mimic the stock set up in that the gear shift sits below the actual footpeg. Most Japanese rearsets have a footpeg with a machined section that the gear shift rotates on so it all attaches to the rearset as one.
That being said......there are some super cheap rearsets on Ebay that have the gear lever attaché at the foot peg like the Japanese ones do. They will have their own shift rod which won't work with your quickshift. Woodcraft, Lightech, Gilles have a separate gear shifter and foot peg and use the stock shift rode/quickshifter so you're good to go with any of them.