synth keyboard acting as midi conroller

Gear involved:
1x MPC 1000 (Soft Thru; As Track or Omni?)
1x Access Virus Indigo 2 (Can turn Local Off and On)
1x Roland JU-06 (module that I want the Virus to control and MPC to sequence)

If I want to first MIDI sequence 2 parts from the Indigo 2 itself (lead & pad) on MPC track 1 and track 2 respectively, then for track 3, use the Indigo 2 as a keyboard controller for the JU-06, is this possible without the first 2 tracks being "muted"? I want the first 2 tracks (from the Indigo 2) to act as live backing tracks for track 3.

Because, once I switch Local Off on the Indigo 2 to use as a keyboard controller with the JU-06, it essentially becomes just a simple MIDI keyboard with the synth engine turned off, right?

So, how can I lay down sequences from the Indigo 2 and later use it as a keyboard controller for my sound modules and keep everything that I sequence before playing?

The Indigo 2 has MIDI In, Out & Thru, if that helps any. I have no clue how MIDI Thru in this situation would work and MIDI in general gives me migraines, so I'd be much obliged for any answers.

1 midi output has 16 channels to send midi information on. So you can use ch 1 and ch 2 to send midi info to the Indigo (on tracks 1 and 2) and have midi ch 3 to go to the juno.

Midi out indigo > Midi in MPC (keyboard and cc)
Midi out MPC > Indigo midi in (midi ch 1 and 2 controlling Indigo sounds)
Midi tru Indigo > Juno (controlling Juno on ch 3)

Or you can use midi output B to go directly to the Juno.

Because, once I switch Local Off on the Indigo 2 to use as a keyboard controller with the JU-06, it essentially becomes just a simple MIDI keyboard with the synth engine turned off, right?

I think you can send back midi to the Inidigo to control it. Look it up in the manual.

yes I do believe the Indigo 2 can receive MIDI, page 111 talks about it receiving data

So referring to your routing example, I can utilize the MIDI Thru of the Indigo 2... by connecting it to the JU-06's MIDI In?

I figured I could use MIDI Channel 06 for the JU-06 (easy to remember the 06's).

So I would I just turn off MIDI Channel 06 of the Indigo 2 and never have to switch Local Off, that way the sound engine would still be triggered by the MIDI notes of MPC tracks 1 & 2, while the current MPC Track would be set to receive on MIDI Channel 06 (ie the JU-06 would be transmitting data to MPC MIDI Channel 06)