I'm no spring chicken Nick so not as smart on a laptop as some but I always do it online now. Remember, you can submit 15 days before so there's plenty of time to give it a go. Of course if you get a new passport you have to go in person the first time.
just open an Immi account. If they need more docs they will request usually. I had a deportation case but got the lady back in. It took a year mind you. Any help I can give is free.
The single most important thing is that she has financial stability / security in her homeland and a solid reason for why she will not stay in Aus. Having kids/ dependent family is a poor reason and can go against the applicant. A letter from an employer, tax submissions (if self employed) proof of assets, land, gold etc can help.
If you come back into Thailand by road it used to be a 14day pass. Only if you returned by air from outside Thailand you get a 30day stay. Have the rules changed?