The sports editor makes his or her choices every day as to content, layout, etc. There's no mandate to run anything over anything else. It's all strictly subjective on the editors' part.
Once everything the State, Ole Miss, JSU, etc. beat reporters has been used, the remainder of the space is filled by the most pertinent AP content, whatever, in the sports editor's opinion, that may be. I presume they're using Auburn and Alabama content over other wire content because they believe there's more interest there.
Every editor has his own criteria. Obviously an AP story about Favre being traded would likely be used more prominently than college practice reports in which everything is mostly routine. Also, with one reporter compiling info on each Mississippi team, pretty often some papers will have a particular day of the week be several stories about one particular team, another day another. Wednesday might be MSU day, Thursday UM day. Or they could use a trickle about each team every day. Whatever the content will bear.