Though the links above and below go to the Chicago quick guide - the full print Chicago Manual of Style is available for more complicated questions. These large print volumes can be found both at the Library Services Desk and in the Stacks.
"Detailed lists of national and local archives in the United States, Canada, Mexico, and other countries throughout the Americas." Also - "Descriptions of and links to various online databases, digitized collections, mapping projects, and online content creators that focus on the early Americas." --- Early American Sources
"The Iowa Heritage Digital Collection is an online repository of Iowa history and culture, maintained by State Library of Iowa, which brings together digital resources of Iowa libraries, museums, historical societies and other cultural institutions to enhance access to and preserve long–term accessibility of these valuable materials." --- IHDC
"In recent years, a number of scholars, researchers, and tribal members interested in New England Native communities have noticed problems with the current state of resources on the topic. Most obvious is a general lack of published primary source materials, despite the existence of thousands of relevant documents. Equally problematic is access to these original materials. Individuals needing to use such items are required to visit a number of repositories, mostly across the northeast. Archaic or poor quality handwriting, or the restrictions placed on worn and fragile papers can further hinder the researcher’s task, making it time-consuming and costly.
Several institutions that have significant New England Indian collections have organized into a cooperative endeavor called The Yale Indian Papers Project to address these problems by publishing an electronic database known as The Native Northeast Portal." --- Native Northeast Portal
"The Papers record far more than the era’s military history. Between 1784 and 1800, the War Department was responsible for Indian affairs, veteran affairs, naval affairs (until 1798), as well as militia and army matters. During the 1790s, the Secretary of War spent seven of every ten dollars of the federal budget (debt service excepted). The War Office did business with commercial firms and merchants all across the nation; it was the nation’s largest single consumer of fabric, clothing, shoes, food, medicine, building materials, and weapons of all kinds." --- wardepartmentpapers.org
There are thousands of publicly available digital archives that could contain useful primary source material for your project. Focused searches using powerful Google commands can locate digital collections based on the descriptions of archives.