The National Archives is in the process of digitizing Record Group 109, Confederate Records. These record books are divided into "chapters" and then volumes. You will see that type of citation in footnotes in any scholarly Civil War book. These are the chapters:
I: Adjutant and Inspector General's Office
II: Military Commands
III: Engineer Department
IV: Ordnance Department
V: Quartermaster Department
VI: Medical Department
VII: Legislative Records
VIII: Miscellaneous Records
IX: Office of the Secretary of War
X: Treasury Department
XI: Post Office Department
XII: Judiciary
Go to the Advanced Search page, in the search term box type "rg 109", and unclick all of the boxes except Archival Descriptions with Digital Objects. Then click on Search. You may want to change to 100 results per page, and if you sort by Local Identifier you will get a list in chapter and volume order. Pick a title and click on it and you will see the cover of the book with thumbnails below for the first thirty or so pages. Be sure to note the slide bar next to the thumbnails, and the Load More and Load All buttons. You will also have the option to enlarge the image and download a full size image which you can then manipulate and print if you like. Of course the quality will vary according to the original.
To limit your results, just add another word or phrase next to "rg 109", such as Texas. Now you are down to 43 results, including appointments of chaplains, telegrams received 1864-1865, record book of the First Texas Cavalry, troops tendered to the Confederate War Department in 1861, morning reports of Col. J. J. Cook's regiment of Texas Heavy Artillery, and Chief Signal Reports from Houston Observatory Relating to Meteorological Conditions and Enemy Vessels, 1863-1864. Most significant locally (so far) are digitized copies of Letters sent by Lt. Col. G. H. Hill, Tyler, Texas, 1864-5 (the ordnance works here) and Miscellaneous Record Book, Little Rock Arsenal, Texas and Tyler Ordnance Works, Texas, 1862-1865!
Of course the books themselves are not transcribed (they are handwritten--quality varies), are not truly indexed, and aren't searchable by word or phrase. Some volumes may have a name index in the front--all of the A's together, B's, etc. Contents are generally in chronological order, as they happened and were written down. Plan on spending HOURS working through the books. But at least you can do it at home, in your jammies, with your Starbucks, and not have to spend the airfare, subway fees and hotel rates to go to Washington, D.C. to see them.
These sites select, organize, and link to other websites.