There aren't rules, per se, about when you're allowed to write the word as it's actually pronounced in the dialect and when you're not. Gaeilge is certainly the standard spelling and it's possible that Gaelainn/Gaoluinn is considered an acceptable alternate spelling in the Official Standard, but I'm not sure. When writing specifically in Munster dialect for a Munster audience, however, Gaelainn/Gaoluinn is perfectly acceptable.

Honestly, the only way to know this stuff is to spend years reading everything you can get your hands on.

Mo bhuíochas (nó mo "bhaochas"?)

Unlike "Gaelainn", bhuíochas, even though pronounced "bhaochas", is the only spelling I've ever seen, no matter the dialect.

I think you run the risk of driving yourself mad if you try to write in dialect right from the start. Obviously it's up to you how you go about this, but I would strongly recommend keeping your written Irish standard. That doesn't stop you from pronouncing it in a Munster fashion, of course.