The Shareholder's association asked similar questions a while ago. I think the reply was along the lines that inevitably some people may be disappointed by whatever seats they're finally allocated, but hopefully the capacity increase and viewing quality of every seat will minimise that.
I think originally there was talk of a simple transposition of season ticket holders en masse as the easiest method... so that whole sections of people are simply moved to the corresponding positions in respective stands...... ie Gwladys St go in the new traditional home end (South Stand) and Mainstand/Top-Balcony go into east Stand etc... with a period for reshuffling for those who might want to change their viewing position at BMD. There was also talk of a tiered system were longer held season ticket holders get first dibs and that fans will be able to have some flexibility in terms of grouping with family and friends etc. Not sure where they are at, but it has the potential to be a bit contentious for some.