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Thank you for the great question. At the National Archives, we tell our transcribers that the most important thing to remember is that transcription should help with readability and searchability. We don't have strict rules about what is right and wrong when it comes to transcription, but the way you transcribed (one column at a time) likely makes the most sense in terms of readability, since you are transcribing just as you would normally read the newspaper.
As for formatting, do not worry too much about matching the exact format of the original document (this includes line or paragraph breaks or spacing). Simply type the words that you see in the document, as every word you transcribe helps improve search results for that document. Whether or not the spacing matches exactly will still return a search for the words in the document. However, it can often help the next reader follow the flow of the document, so use your best judgement to see if formatting helps make sense of the document.
I hope that is helpful as you transcribe. Thank you for your contributions as a Citizen Archivist!
Community Manager, National Archives Catalog