What should I do after entering Thailand on a tourist visa while holding a work permit and non-B visa?

I recommend you to apply new visa with current work-permit. After getting new non-b, you have to cancel your work-permit and apply new one. By the law, your work-permit is already expired because you entered country with tourist visa. Immigration officer and labour officer is very stick about this. You can't convert type of visa, extend visa and renew work-permit.

You should apply for a multi entry. I cannot remember the cost my company paid it, maybe 3-5k Baht

You canceled your 90 day Non-B when you left the country.

You didn't come in on a 30 day tourist visa because there is no such thing. You came in on a 30 day visa exempt entry.

IF your company can provide the documentation you can go to the immigration office in your area and apply for a 90 day Non-B visa BUT you need at least 15 days left on your current stamp to do so because it would go under consideration for 14 days before you went back to get the Non-B and the new 90 day stamp inked into your passport

OR

You take documentation from your company and you go to a thai consulate in a neighboring country to get a 90 day single entry Non-B again.