With the engine running you need to put the timing lead on the #1 cylinder spark plug, loosen the distributor mounts and twist the distributor housing until the timing marks line up like they tell you to in your repair manual [you do have a repair manual right?]. You will be pointing the light down at the crank pulley, and the marks will line up with a scale on your timing belt cover. You don't have to reposition the timing belt or gears any specific way. If the engine runs fine, the cam timing should be fine, just check the spark timing.
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-Harry
AIM: NDcissive
CRX and Pre '92 Civic, Engine Tech and Tuning, & Track and Autocross Forum Mod