Lewis and Clark, like Abraham Lincoln, like the American Civil War and so many other topics in American history have spawned an extensive collection of literature. Some of it may be helpful to those with an interest in the military aspects of the expedition, but much, while fascinating, is not useful. I'd like to offer some suggested reading.
First-always first-are Lewis and Clark's journals. There were several different editions of these journals-first Nicholas Biddle, then Elliott Coues, and lastly Reuben Gold Thwaites. These have all been superseded by those edited by Gary Moulton at the University of Nebraska. Twelve volumes, about 50-60 bucks a pop (except for the Atlas which is volume one at $175.) I know because I own them all. However there's been a recent development. These are all on-line, thanks to the National Endowment for the Humanities and the University of Nebraska Press, among others.
The journals are very searchable by date, so you do kind of need to know what you're looking for. The atlas is also available and very easy to use. (Mine is enormous and I can only look at it on the kitchen table.) The site is also chock full of great illustrations, audio files, you name it. I spend hours there. It is an incredible gift to those interested in the Corps of Discovery.
Another equally wonderful on-line resource is the U.S. Army's site devoted to the Lewis and Clark Bicentennial. It covers the Army's activities during the bicentennial (2003-2006.) However it also provides little snapshots about every member of the Corps of Discovery from the captains to the NCO's and enlisted personnel, to the boatment who hired on. There is also a great little section devoted to uniforms and what the men might have worn when they weren't in dress blues. It's another site that is totally worth your time.
I've added both these sites to my list of useful links.
Last, but not least, I'd encourage you to take a look at the historic art of Michael Haynes. He has done a fabulous job of capturing Lewis and Clark on canvas. He has a series of Osprey-like color plates, and then has gone on to illustrate the Corps in its various contexts, whether recruiting at Fort Massac in 1803, breaking a mast on the keelboat, or stuck in the Dismal Niche at the mouth of the Columbia. I've also included this link. You should find it useful to determine what the soldiers wore and the equipment they carried. Haynes also illustrated a wonderful book on the Corps of Discovery called Tailor Made, Trail Worn by Robert J. Moore, Jr. Not a cheapie by any means, but I've gotten a lot of use out of it as I work on this project. It's available from Amazon.