These three things are found in the body of the Church, just as they are found in a natural body, namely, the mystical body itself, its chief members (prelates and rulers) and the head, namely, Christ, from Whom life flows to all the members. Some of the epistles deal with the grace of the New Testament, so far as it extends to the whole mystical body of the Church. This is a theme of all the epistles he sent to the churches, i.e., to the Romans, Corinthians, Galatians, up to the first epistle to Timothy. In others he treats of this grace, insofar as it extends to individual persons, namely, Timothy, Titus, Philemon. But in the epistle to the Hebrews he treats of this grace, inasmuch as it pertains to the head, namely, Christ.
He also makes more clear the breakdown among particular Pauline epistles in his Commentary on Romans. The basic structure of it is as follows.
I. THE CHURCH AS THE MYSTICAL BODY
The first series of epistles have to do with God's grace:
Romans: describes God's grace (which works sacramentally)
I Corinthans: describes the sacramental life of the Church
II Corinthians: describes the ministers of the sacraments
Galatians: excludes superfluous sacraments, against those who want to mingle old and new sacraments
The next series of Epistles have to do with the faith of the Church.
Ephesians: for the fortification of the faith of the Church, particularly by describing the unity of the faith
Philippians: for the growth and preservation of the Church
Colossians begins the theme of protecting the faith:
Colossians: for the protection of the Church from corruption and error
I Thessalonians: for the protection of the Church from present persecution
II Thessalonians: for the protection of the Church from future persecutions, by warning of the Antichrist
II. THE CHURCH AS COMPOSED OF INDIVIDUALS
The first three have to do with the individual as having responsibility in the Church:
I Timothy: with regard to the unity of the Church
II Timothy: with regard to the steadfastness of the Church against persecutors
Titus: with regard to the protection of the Church from heretics
Philemon adds to this by helping us to understand the role of the Christian who has temporal responsibility in the world.
III. CHRIST AS THE HEAD OF THE CHURCH
Hebrews is the pinnacle of the ecclesiology, for it discusses Christ, the Head of the Church.
Of course, Aquinas doesn't think the above themes are the only things found in the epistles; it's just that, by seeing the epistles thematically in this way, we can see that the Holy Spirit, by giving us Paul's epistle, has given us a complete study of the role of grace in the Church.
You can read some very good translations of some of Aquinas's commentaries on the Pauline epistles online in PDF format.