The problem you are experiencing I doubt very much is a bank problem nor a transfer problem it's a promptpay problem which is independent from the banking system. It typically has issues like you stated. You tried to pay a different bank hence the issue. Best advice is to open an account at ALL the banks and if you have trouble paying just transfer the funds into the bank account of the same type you are trying to pay for. This also has another advantage, that is you don't have to go finding your particular atm as you have all the banks.
I was on an ED visa for 5 years. Never had a problem with subsequent visas. Even had a denial of entry cause I was border running. Didn't affect my application.
You can work online legally under any visa as long as you're not working for a thai company. Either way if you don't tell em you're married to a thai they won't ask.