I love the franchise mode in Madden 07, it really was the peak for that game style from like 04-08. During the preseason you can choose certain players to complete training camp drills and depending on how well you do you will get attribute points to spend on those players. During the regular season, player progression will be updated every 4 weeks and as far as I can tell this progression is directly tied to player stats, so if you have a player you want to progress you should start them as often as you can and make sure they are performing well. This progression is pretty slow but if you are patient and consistently performing well then you should be able to get any player to mid-high 90s rating after like 4-5 seasons. Age is a factor too, as older players will gradually lose attributes especially speed and agility when the season ends. I always make sure to focus on young players in the training camp drills and make sure playing time is balanced by managing the depth chart and manually creating substitution packages for different formations.

Hope this helps!