For the timing strobe, positive clamp on positive at battery, negative clamp on ground or negative at battery. The other weird clamp is an inductive pickup. It senses the spark pulse through the spark plug wires by way of magic. With your bike idling and the special clamp over either the #3 or #4 plug wire, point the gun at the timing window in the points plate and pull the trigger. You should see the F mark lined up with the witness mark on the case. If your special magic clamp is on the #3 wire then you'll see the marks for the 2-3 cylinders. If the clamp is on the #4 wire you'll see the 1-4 cylinder marks.
Then, rev the motor to about 3k rpm and you'll watch the marks move counter clockwise. Then the advance marks should appear and match the witness mark. There are two advance marks, just get them to straddle the witness mark on the case. Do this for both 1-4 and 2-3.
The advance setting is more important than idle setting. So if the advance is good but the idle F Mark doesn't line up exactly, no worries. But with properly gapped TEC or Nippon Denso points and plate they should be good.
Search YouTube for "timing strobe" and you'll find videos.