There are a couple different ways you could split sounds to different channels, sending the Tonic Pad to one, and a keys sound to another or a metronome. You could do this by panning all the keys sounds right and the tonic sounds left, but a better way would be to setup an audio aggregate device for Tonic, and keep the keys in stereo. This video shows how to setup this to use a click, but you would do the same process just use the Tonic channel strip instead of the metronome.
If you don't have an audio interface, and you want the metronome separate for recording there are a couple choices. The headphone jack on your computer is the “Built-In” output. This is considered 1 stereo out. So if you wanted to separate click and keys, the only way using just the headphone jack is to pan all the keys channel strips hard left, and the metronome channel strip hard right. Then you can use a cable that is 3.5mm to 2x 1/4” TS if you want to send those 2 channels to a sound console/mixer. The cable splits the left and right signal so you have one with the keys and the other with the metronome. You could also separate the left and right in software if recording. The MainStage record button is pretty limited, it will just record your final output, you can’t record multiple tracks.
If you have logic then you can copy the patches and play them in Logic and then you would be able to use the logic metronome to record to but won’t bake that into your keys tracks. If only using MainStage I would probably just recommend a metronome app for your smartphone, or even just google metronome and you can use the one built into google search.