Hi,

I'm going to be recording with my cousin who is a professional singer and "semi pro" recording engineer that uses Pro Tools. I have absolutely no experience with pro tools, and thought maybe some of you have some experience or knowledge.

First I was wondering if parts played on an arranger using auto accompaniment can be separated so later they can be adjusted for volume EQ, compression and other effects, or maybe even replace some of the auto accompaniment parts with live instruments?

My cousin will be getting into town next week, and I'm sure once we talk face to face he'll understand better and be able to answer my questions. He never worked with an arranger keyboard so it should be an interesting learning experience for us both!

What is the Arranger model?

Most likely a Ketron Audya 5. Maybe a Yamaha 950.

Very possible. You can only separate the tones if you record MIDI (not audio), and Pro Tools can do that. If the local sounds (on his computer) do not sound the same to you, you can reroute the midi signal back into the Yamaha for mixdown during playback. In reality, it's almost easier to create the mix you want on the kb, itself, then record the audio in stereo to Pro Tools in a single pass.
If you kb has separate outputs, you can isolate as many sounds/groups as you have outputs.
ie:
If you have stereo mains, and 2 aux outs:
L/R - main mix of arranger tracks
Aux 1 - Bass
Aux 2 - drums

Or, any combination of the above that suits your needs. Have fun. I love working in the studio. I actually plan to spend a lot more time in mine in the coming year.

That is exactly what I intended on doing but my cousin says that he thinks we'd get better results recording each instrument separate.
He has always recorded full live bands though...

Perhaps, but if you like the arrangement you pre-record, you save studio time, and $$$ by doing it before hand. It's all about the final mix - do you really need that precise control after the fact? If yes, then use MIDI.