Hi Josie, I'm at this stage on my Dory. I assume the track is in those lengths because those are the standard lengths from the manufacturer, and CLC doesn't trim each piece, allowing the builder to determine the exact trim for their boat. For instance, I shaped my mast a bit slim at the top, so I'm moving the gooseneck down so the cheek block can be positioned lower to give it enough wood to handle the loads.

To answer your question, place the shorter length of track lower on the mast, so that the joint between the two tracks is reachable if the sail gets hung up there. The manual advices using a metal file on the track ends so that happens less (and lubricate with paraffin wax). Use a hacksaw to trim the track flush with the top-end of the batten, but make sure that it's high enough so that the top sail car doesn't come off when the sail is hauled all the way up. A dry-fit of your sail would help.

And bear in mind that the track is supposed to cover the gap in the batten. The loops in the stays will be slid over the mast and sit in that gap before you screw on the strack. You can install the eyestrap after. 

   Thanks Will! U. We did cut it and did just as you suggested with the shorter piece lower. We are inexperienced enough that we hesitate to do anything if it is not explicittly stated in the directions but as we come to the end we are finding everything more confusing. Rigging will be our next challenge. We were advided by CLC to put our micro cheek block up as high as we can even though my son sanded the last few inches of the mast to a thin broomstick thickness. We were told it should be strong enough so ours is placed at a spot just barely wide enough for the block with no excess wood on each side. That way the gooseneck didn’t have to move. Reading other comments I got the feeling that you want to avoid moving the gooseneck. 

   Ah, well good to know. I lost a few inches off the top of the mast due to a runaway router, so I'll keep it high. I'm going to dry fit the sail to make sure. Good luck in the final stretch!