Option one: close mic each instrument separately and put a baffle in between the two players. Send it to your sequencer.
Option two: Use ambient room mic and allow for "bleed" between the two instruments.
If they are tightly together, and there is no need to correct each track, it won't matter much if the mics are placed correctly.
Option three: Record each instrument one at a time and mix it on the computer.

A lot has to do with 1. how well the players work together 2. The predominant sound you want 3. whether you care about the "bleed" from one track to another.

The techie you talked to obviously didn't know about music recording.

For a final, bounce your program on the sequencer to iTunes and burn a CD.

I would recommend saving independently recorded tracks to a storage area, a CD or a USB drive in case you want to bring it to a mastering engineer.