Complex sentence: They simply did not play well enough at the time of their conference tournaments, and often at-large berths will get higher seeds than the teams that beat them in the conf. tourney, simply because the Selection Committee judges based on the entire season.
Split into simpler sentences: They simply did not play well enough at the time of their conference tournaments. Often, at-large berths will get higher seeds than the teams that beat them in the conference tourney, because the Selection Committee judges base their judgment on the entire season.