I'm in a 12-team dynasty league that starts 11 offensive players and 11 defensive players (4-3-4 or 3-4-4). We keep 6 offensive and 5 defensive players. According the VBD principles, you should begin deviating from the VBD after the 100th pick. Technically, we're WAY past the 100th pick at the start of the draft!
Should I simply start by placing more importance on positional needs?

Yes, for the most part... I'd still peek at the VBD to see if you can fill any of the positional needs based on value.