Back when I was working on my first book, the internet was just becoming popular. At the same time, I was working in the library at the Watauga Campus of Caldwell Community College. One of the biggest pieces of advice we gave our patrons was that unless the information came from a credible source, they should not use it. While I left the library a number of years ago, the same thing is still true: be very wary of information, generally speaking, that you find online.
That being said, there are a few online resources that are incredibly helpful to a researcher/writer. I will not cover every site that I use, just a few of them.
Probably the two most useful are the Making of America site and fold3.
The Making of America (MOA) is a "digital library of primary sources in American social history from the antebellum period through reconstruction." I use this site the most to access the War of the Rebellion: A Compilation of the Official Records of the Union and Confederate Armies, often referred to simply as the ORs. There are 128 volumes of ORs, and, thanks to this web site, they are all searchable. You will find within the ORs the reports of officers after the battles, general and special orders, and communications between officers. Of course, not everything is in the ORs. Some of it is still lost, but I would consider this source indispensible. You can access that database here, and it is free! As an aside, several years ago, Broadfoot published a Supplement to the Official Records, but that is currently not online.
While MOA is free, fold3 is a subscription database. It is the best money I spend every year. Fold3 has an incredible amount of material on it, but I primarily use it to access the Compiled Service Records of Confederate soldiers. In the past, if you wanted the look at your ancestor's compiled service records, you had to either write the National Archives, or visit one of the libraries that had the information on microfilm. For me, that meant going to Salisbury or Raleigh. Fold3 has all of that information digitized. You go to the site, and click on Civil War, compiled service records, Confederate, North Carolina, Thirty-seventh regiment, and say, the letter B to access all of the soldiers in that regiment whose surname start with the letter B. If you are going to write a regimental history, you need to go through every single slip of paper. You can find returns for equipment and food, extracts from court cases, resignation letters, and all kinds of bits and pieces that will make your project that much more interesting. You can also access the Compiled Service Records for generals and their staffs - do not over look these files! Is it time consuming? Yes! But it pays off. You can access that site here.
Probably the other sites I use often are historic newspaper databases. There are several. There is the Library of Congress site, which is very easy to use, but they have no North Carolina newspapers on it right now. There is also a site from Archives and History that has the war-time Salisbury newspapers, but I find this site hard to use. These two sites are free. Other sites, such as www.newspaperarchive.com and http://www.genealogybank.com/ are also good and have North Carolina newspapers, but these are subscription sites. I use as many different sites as possible, and I look broadly. At times, veterans moved off to other states after the war, and left reminisces of their service in their new hometown newspapers. Once again, this is very time consuming, but it often pays off!
The other set of resources that I find really helpful are online book databases, like Google books and NetLibrary. When I was researching the Civil War Charlotte book, I sat down with Google books, and typed in "Charlotte, North Carolina, 1861." I went through every year of the war, while also using terms like "Civil War," "Reconstruction," etc., etc. There are tidbits hidden in books to which I normally do not have access. Once again, it just takes time to find them. At times, Google books will only give you a rough idea of what is in the book, but at least I know that the book exist, and I can go and find the book through traditional means (like a library).
A final set of online sources might the family surname and county list. With both my projects on the 37th NCT and 58th NCT, I sat down with genforum.com and posted the names of every single soldier that served in those two regiments, telling folks what I was working on and asking for their help. It took months (there are somewhere around 4,100 men who served in those two regiments). However, I found unpublished letters, diaries, family stories, and photographs that are not in the traditional places (like libraries). Plus, I generate a list of people who might be interested in purchasing the book. You will need to think about this type of time commitment; maybe just posting the names of officers and/or NCOs will be enough. The biggest thing here is getting the word out about what you are working on.
Be careful about using information found on general web searches. There are a whole lot of people who write things about their ancestors and post it online who really do not have a clue about the war/military life/civilian life, etc. They mean well, but may not have the background to properly interpret what they have read or been told. For example, I once read that times were really hard during the war years because this person's ancestor only got paid every two months.... Well, the war years were hard, but according to military regulations (North and South), everyone only got paid every two months.