Hi @MDrake,
The typical way in JMP to perform a paired t-test using the Matched Pairs platform, which is available under Analyze > Specialized Modeling > Matched Pairs.
A less common way to perform the Paired t-test is using Fit Y by X just as you have before (with a continuous Y variable, and a continuous X variable), but before clicking the Red Triangle, hold down the Shift key on your keyboard. You will see the Paired T-test option now available in the menu. TheMatched Pairs platform has more options, but occasionally it's useful to run the Paired T-test through Fit Y by X.
I hope this helps,
@julian