While there are some fine resources on religion in the Civil War, there is a dearth of material specifically on Confederate chaplains. I would encourage your research in this area. Here are a few resources that I know of (aside from Charles T. Quintard which is an excellent resource and has already been mentioned):

While there is not a book on Brigadier General Mark P. Lowrey, there is quite a bit of material about him if one researches. While Lowrey was not a chaplain, he was a Baptist preacher in North Mississippi before the war and continued with phenominal results after the war. He did preach to his troops on occasion. Larry Wells Kennedy wrote a Ph.D. dissertation at Mississippi State University entitled: The Fighting Preacher of the Army of Tennessee: General Mark Perrin Lowrey

Chaplain James McNeilly of the 49th Tennessee Infantry has several articles published about him in the Confederate Veteran. He was a very interesting person and deserves more attention.

James P. Boyce was a Confederate chaplain and later was the president of The Southern Baptist Theological Seminary in Louisville, KY. Their archives should have a great deal of infomration on him.

William J. Jones. 1887. Christ in the Camp. (Outstanding primary resource)

William A. Bennett. 1877. A Narrative of the Great Revival
Which Prevailed in the Southern Armies During the Late Civil War Between the States of the Federal Union (Outstanding primary source - gives great information about the work of chaplains in the Civil War).

Henry Lee Curry, III wrote a book entitled God's Rebels: Confederate Clergy in the Civil War. 1990. Huntington House, Inc.

Here is an on-line article about Confederate chaplains.
http://www.rmjc.org/pdf/confederatepreachers.PDF

Steven Woodworth, history professor at Texas Christian University, wrote a book a few years back on religion in the Civil War entitled: While God is Marching On. I would scour his bibliography for additional resources.

Another book, written by Sidney J. Romero, Religion in the Ranks, 1983, University Press of America

In addition, here are a couple of theses and Ph.D. dissertations that you might find helpful (I would pay particular attention to their bibliographies for additional sources):

There is a master's thesis written about Isaac Tichenor, Chaplain of the 17th Alabama. I don't remember off hand what school the thesis was written at, but it should not be too hard to find. At Shiloh he picked up a rifle and joined the fighting winning the everlasting respect of the men of that regiment.

Born Again in the Trenches: Revivalism in the Confederate Army Ph. D. Dissertation by Gorrell Prim at Florida State.

The Religious Awakening in the Army of Tennessee M.A. Thesis Duke University by James Allen Crisp, Jr.

Rebirth of An Army: The Confederate Army of Tennessee At Dalton, Georgia During the Winter of 1863-1864 B.A. Thesis at Georgia State by Scott Dobson

This is all that comes to mind right now. Contact me if I can help in any way. I have studied religion in the Army of Tennessee quite a bit.