I think no matter how they run the changeover a certain group will be disadvantaged, that's just a fact of life in this situation. The most likely method will be positions on pure seniority. They could pay a large number bypass to keep the current domestic pilots on the new type but that would most likely outweigh the cost of double training ie, training a 737 F/o to S/o and an S/o to A320 F/o as opposed to just a 737 F/o to A320 F/o.
When the 737 departs all new hires will have to be S/Os as that will be the lowest pay scale and the only entry level position.