The Project5 Help file contains the following lines:
Well, yes and no. Let's use all of this information together to invent some useful tricks with the Arpeggiator that extends the functionality. Load up a synth to P5, enable the Arpeggiator, and create an additional Track Layer. Click on the 1.1 layer, and Transpose the layer down one octave to -12. Keep the Arp's Ch setting on 1, and change the Track Inspector setting Send To: Channel 1 for this layer only. Back in the base track, switch the MIDI Sent To: to a channel other than 1. Your base octave for the Arp is now one octave lower confined to it's own layer and your original chord will ring through on the main track.
For independent control of each layer, there are several ways to separate the two. One method involves using the Qwerty shortcuts. Go to the the Options menu and tick the MIDI Override Follows Track command. Toggle the X key on your Qwerty to enable/disable the MIDI Override on the current track, and use the Up & Down arrow keys to switch tracks. Now you can have the original chord, the low octave arp'ed line, or a combination of the two at your fingertips. If you Arm both the main track and the layer, you can record the jumps from Arp-only to chords to a mixture of both across the two layers. Keep the resulting patterns separate; Combining Selected Clips will negate the performance playback nature of the Arpeggiator.
You can also get a mix of original and arp'ed sounds by using the Chord Mix control, but without the transposing shifts that this layering technique provides. Keep in mind that each layer has a unique Track Inspector, where you can set different Transpose settings for each one. The Send To: [MIDI] Channel in each Track Inspector and the Arpeggiator Channel setting for the layered group can be set independently of each other. That opens up a lot of possibilities, especially considering that the Arp can have multiple processing channels enabled at once. These 16 channels can all be ticked individually, or overridden with an All channels setting.
This article details a single transposition on a single layer, but the same principles apply with multiple layers/transpositions. You can use any semitone value from -127 to +127 steps, shifting your Arp independently from your input source, or shift only the original input without affecting the arp's base octaves. And this process is available independently for each Track Layer added.
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