I hunted down Bertram Hawthorne Groene's Tracing Your Civil War Ancestors in hopes of finding a good Civil War genealogy textbook. Unfortunately, the book is very dated, despite having been reissued in 1995. Of the eight chapters of Groene's work, all but "Acquiring and Identifying Civil War Equipment" should be of use to Civil genealogist. Most have to be approached with great caution now.
In the section on the National Archives, I would recommend only the first page. That page provides an outline of the records available onsite. The remainder of the section describes, in great detail, the use of NATF Form 80. The genealogist attempting to use Form 80 would find themselves lost. It is no longer used by the Archives.
The section on the state archives is, sadly, completely unusable to the genealogist. It recommends that one write a letter to the state archives, requesting all information that they may have on a specific soldier. While most archives would respond to such a letter, the results may be lacking. One needs to know what records exist to be sure that they have all been consulted.
Of great use to the genealogist is the section on the Official Records. Made up of various publications of the Army and the Navy, these publications are usually forgotten by genealogists. They're well worth your time - as I hope you'll discover for yourself.
The final sections of the book refer to publications on the war. Many may still be of use, if you're willing to wade through the long list offered. I'll admit I skimmed this section.
While I will not be using this work as a textbook, I would recommend it to a newbie. It's worth a look.