Well, then you select your instrument from the side chain menu to be the trigger. For midi controlled software instruments it's a little different.
From the Logic Pro 9 User Manual:
Knowing Where Different Plug-in Types Can Be Used
Keep the following in mind when inserting plug-ins into channel strips:
Effect plug-ins can be placed in the Insert slots of all audio channel strip types (audio, instrument, auxiliary, output).
Software instruments can only be inserted into instrument channel strips. These channel strips feature an Instrument slot, directly above the Output slot, which is used for software instrument insertion.
Audio Units Generators can only be inserted into instrument channel strips.
Audio Units MIDI-controlled effects are inserted into the Instrument slot of instrument channel strips. The audio signal that you want to process is then selected via the plug-in’s Side Chain menu.
Here are also a few examples involving side chaining for different purposes…..
http://audio.tutsplus.com/tutorials/production/quick-tip-lock-your-chords-to-you r-groove/
http://audio.tutsplus.com/tutorials/production/programming-rhythmical-gates-in-l ogic-pro/
http://audio.tutsplus.com/tutorials/production/how-to-create-an-80s-gated-reverb /
Have a nice day