Hi! I had to manage the meeting myself suggests that you are trying to say that you and no one in place of you, had to manage the meeting, whereas I had to manage the meeting 'by' myself indicates that you were the only person available who managed the meeting. 'by myself' in my opinion, is synonymous to 'on my own' or 'without any other person's support or contribution or help' . Thanks Syed

My opinion is that both are correct and there is no difference in meaning.