Thank you very much for your interest in learning our language, Vietnamese.
You are right when you say that there are three main dialect regions in Vietnam. But, you don't have to worry about choosing the dialect to study. Because the Vietnamese taught in all websites is Standard Vietnamese even though the teachers may be Northern or Southern. They don't teach dialects. The difference is only in their accent.
So, please choose any source that you like, any material that you find interesting for you to learn. You can understand Vietnamese no mater the speaker is Northerner or Southerner.
After the year 1975, there were a big movement of people from the North to the South. So nowadays, Northern dialect is easily to understand in the South and vice versa. As for me, I come from the North but I don't find any difficulty in listening to the people come from the South or even the Central areas.
I would like to recommend to you a website for learning Vietnamese. The speaker is Southerner but teaching material is 100% standard
Wish you success in your language study.