To properly synchronize a plugin/bidule, certain criteria has to be met:
You can choose from four native bidules to generate a master tempo:
However, there are also a few third-party VST plugins that can generate their own internal tempo: (please contact me if you know a plugin that should be added to this woefully short list)
The following tutorials demonstrate:
A how to synchronize a VST plugin to a Step Sequencer bidule playing a drum line,
and B how to use multiple master tempos at the same time.
Connect the MIDI output from the Step Sequencer to the input on the AnalogKit. Hold down CTRL and drag the first audio output from the AnalogKit to the first input on the Mixer bidule. This should connect all of the outputs to the Mixer. Finally, connect the Mixer's outputs to your audio interface (or to whatever is in front of your soundcard output).

Double-click the Step Sequencer bidule to open it, and resize it so that it only shows the relevent notes in the top octave. Program in a one-bar drum loop.
When the loop is ready, press
on the Step Sequencer's toolbar to play the rhythm, and close the GUI.

If your drum loop is still playing, you can hear that the audio is just passing through SupaTrigga - the plugin does nothing until it is synchronized. You can tell that it is not synchronized because the letter s next to its bidule has no number.
To synchronize the plugin, right-click SupaTrigga, and select Sync to > MIDI Step Sequencer. Start the sequence playing (if it isn't already). After one bar, the plugin will start cutting and rearranging the beats.

Increase the granularity slider from 4 (slices/measure) to 16 (slices/measure). Listen for a bit, then double-click the Step Sequencer bidule. Click in the BPM text box, and change the tempo to 75 (don't forget to press Enter to accept the change). Listen to the changes to the rhythm now.
Return the tempo back to 120, and set the granularity in SupaTrigga to 4. If you like, save the layout as Sync Tut.bidule so you can use it for the second part of this tutorial.
(Click here to do it now)