These ratings indicate a player's relative familiarity with a particular formation and ranges from 1 - 100. The Formation IQ affects the player's ability to utilize his skills when playing within the associated formation, and in general provides about a 5% swing in their Blocking, Tackling, Hands, Game Instinct, and Technique ratings when playing out of the associated formation.
A player's Formation IQ may improve based upon the amount of formation practice you set up for your team. If you do not practice formations, then Formation IQs will not improve - but neither will they decrease. A player's improvement rate depends on his current Formation IQ, as it is tougher to raise higher values, his GPA, and his Work Ethic. Finding the right balance between formation practice and positional skill practice is up to you.
Special Teams rating is a rating that affects how your team performs on special team plays, such as FGA and kick-offs. In general, this is used as an average for your team based on all of your players rather than selecting specific players for the special teams play.