Ok you put in a new timing belt and set the shaft to tdc marks which are at about 1 o'clock on a 1999 Hyundai accent but when you turn it over its a rough idol?

The cams need to be lined up at their respective marks also, if this was done then look for loose connections, bad plugs, clogged pcv, or possible damage to the engine when the other belt broke. Normally after you put back the timing belt, you have to check or adjust the ignition timing. If timing is not right a rough idle is the cause.