Working as a paid employee for a non-profit is about the same as any other legal work for wages when it comes to getting a visa and work permit.
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Have the HRM person from the Non-profit go to the labor office and find out what the labor office want specifically for the letter of authorization to allow the non-profit to hire you as a paid employee. Requirements will vary depending on the nature of the NGO and their sponsorship / authorization to operate.
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Once you have the letter then it is off to get your non-B (you are a paid employee) or diplomatic visa (if it is a government sponsored NGO).
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Once you come back you get your Work Permit and visa extension.
ED visa to study at a uni = no problem for 4-6 years. BA-anything in a Thai uni. 9 credits per semester (9 classroom hours per week - 32 weeks per academic year).
BA in Thai if you legitimately want to learn the language. Most Thai unis are under 50k baht per year and the visa extensions are good for a year at a time not 90-day stretches. You just need to show your transcripts and enrollment confirmation each year.
ED visa to study at a Thai Language center... it is problematic and full of hassles due to flagrant misuse of the visa. Good for a year or maybe 2 on 90-day extensions.