What should I do about overstaying my visa in Thailand, and what are my options for a border run?

Hello everyone. I entered Thailand by air, got the 30 day stamp and then an extension. I was also waiting to get a new passport by mail as mine ran out of pages. I was under the impression that once my passport came I'd be able to change the stamp to my new one and apply for another extension (knowing it would be denied) and be given seven days to leave Thailand.

When I went to immigration today they transferred the stamps but said I cannot apply for another extension as I initially had the 30 day stamp (not tourist visa) and already got one extension for another 30 days. I would have done a border run or got a tourist visa before this extension finished, but I was waiting to receive my passport by mail. To top it off, my family is here from the US so I am trying to figure out the quickest way to maybe do a border run. I know that now I am going to have to pay at least one day over stay - how bad is this? They will be here for three more days - would it make a difference in how bad it looks if one day versus three? Also what is the best border to cross from Krabi and can I exit/re-enter the same day? Thanks in advance for the advice!