That's the Set Measure/Beat At Now feature, which is technically part of the Audiosnap suite of tools, but can be accessed independently by Shift+M in X3.
I often don't even open AS palette or view transients to use this, but the easiet way in X3 is to set the Edit filter dropdown in the track header from Clips to Transients. And 'A' alone opens the palette in X3.
either way, you can Tab, Shift+Tab forward and back between transient markers, whether they're showing or not, and use shift+M to open the Set Measure/Beat dialog. Also, since transient detection may be a little off in some cases, you should keep an eye on the alignment, and reposition the Now time with snap disabled if necessary to get right on top of the transient attack in the waveform. This may require some zooming in and out as you work.
I usually start by counting out 8 measures or so while listening to playback, and setting the downbeat at 9:01. This gives you an average tempo that will get everything roughly aligned to start. Then you can go back and set additional points as necessary, depending on how tight and regular the performance was. Often just setting every 4 measures, or at most every measure is all you need.
Also note that you can set fractions of beats. For example, if it turns out that strongest hits are on the third eighth note of the measure, you can set beat 2.5.