You have a couple of options.
(1) Let the software autoID the motion detector and photogate. The default experiment length will be 18 seconds. You may want a shorter experiment length, e.g. 5 seconds. If so, change it. Click the Collect button and collect your data. It is essential that you let the software run to the end of the experiment, e.g. 18 s, 5 s, or whatever you've set it to. If you click the Stop button early, the photogate times will not appear in the data table.
Now take a look at the data table. Your first column will be time. The next three columns will be the data from the motion detector. The fifth column from the left will be the Gate State for the photogate. Scroll down through the data and you will see rows that show the change in the gate state along with the corresponding times. A gate state of "1" means blocked, and "0" is unblocked. Use the corresponding times to calculate how long the gate was blocked. Ignore the distance, Velocity2 and acceleration2 columns.
(2) We created a file that works and does not include the extra photogate columns. Also the bottom graph shows the Gate State and corresponding time. This file requires that you connect the motion detector to DIG 1 and the photogate to DIG 2.
TIL 1422: Vernier Photogate (VPG-BTD) Troubleshooting and FAQs
TIL 3862: How do I collect data using a Motion Encoder and a photogate simultaneously?