From the horses mouth:
PJ addressed this issue, I believe it was one of his press conferences or radio shows--mid season, or a little bit later. Some enterprising soul could look this up, but I'll just tell you what I remember:
1. Said Cox was playing out of position at A-back, but said he had to get him on the field because he was one of the best backs. Expected him to move back to B-back next year.
2. Said if Allen is one of the best backs he has next year, he will have to look at how he could get both guys on the field next year.
Given that PJ has ALREADY played a guy "out-of-positon" because he wanted his best players on the field, and given that he's indicated he may want to do so next year, here's how I see it shaking out:
We are DEEP at B-back. PJ won't waste that talent: Why deep-six Watson and Cox behind Dwyer and Allen, when 3 of 4 of those guys have A back skills? That wastes talent and does not develop depth. Watson and Cox are very capable back ups at B-back.
So of Dwyer & Allen, who do you cross train? I say Allen. Dwyer can hit a homerun on any play, so his touches need to be maximized. Allen played B-back in HS, and can slide back to B-back if Dwyer gets hurt. Watson & Cox provide very capable rests for Dwyer. Kelly provides depth.
The other argument one could make is that Dwyer has the better skill set for A back. He has blinding speed, he can block (made several nice ones for Josh on QB draws or passes), and he's shown good hands. But in the end our offense is a homerun offense, so Dwyer needs to be on the field more than anyone.
Of course, this is all speculation. It will be determined by who earns what and who stays healthy.