You probably can't reserve golden days until you're released from IOE, but no harm in trying. IF schedplus doesn't let you do it, call CS. It's possible but not too likely that all available golden days are already taken on your desired days.

I'm currently waiting for IOE to start, but would like to do some observation flights in the mean time. I understand I have to arrange this myself, but are there any set protocols to follow?

You just jumpseat on random flights. So just see where you want to go and get on.

Check the loads for your observation flights. Meaning don't try to jump on full flights because you might keep an "other airline" guy from getting to work.
Also somebody might bump you from the jump on the return flight and boom, welcome to Paducah.

This.

Company policy I think is that trainees have priority over commuters for the JS.

My policy (and most CA's I think) is that the commuter has priority because the trainee has options as to when/where to do his flights. Apply common sense and choose less-than-full flights. I will leave you at the outstation and take the commuter.

It does not say anything in the FOM about a SkyWest trainee having priority over a SkyWest commuter.

Same!
................

Dude when is MSP gonna start showing some openings on the CA side again?

What a delightful attitude.

I believe it was a memo a few years ago. Maybe they let that one quietly die on the vine.