Following Harpers Ferry, governors of Southern states petitioned for arms to be sent from U.S. armories at Springfield and Watertown, Mass. Where U.S. armories in their states existed, such as the Mount Vernon arsenal near Mobile, arms were transferred there. In other cases, such as Mississippi which had no U.S. armory, governors asked to purchase modern firearms from the War Department.

For example, on Jan. 28, 1860, the War Department authorized transfer of 5,750 cases of arms to the Charleston, North Carolina, Augusta, Mount Vernon and Baton Rouge armories. Each case included twenty arms, weighed 300 pounds and occupied ten cubic feet. It's safe to say that all of these eventually found their way into Confederate hands.

Also, to arm the different state and territorial militias, the War Department issued arms on an annual quota system based on number of representatives in Congress. The law was passed on April 23, 1808. For instance, during the year 1860 the State of Florida received 100 U.S. rifled muskets, cal. 58, valued at $13.93 each, and 132 cavalry sabers, assessed at $8.50 each. Obsolete weapons such as flintlocks were not issued, and southern governors sometimes asked to draw on quotas for the future, such as 1862.

Of course before the war governors of Southern states could and did send agents to New England to buy arms. Unfortunately they had to compete with Italian agents who were attempting to buy arms for their own civil war. Many arms requisitions had already been made before southern agents arrived. Nevertheless, new England arms merchants were still attempting to ship arms south even after secession.

http://www.simmonsgames.com/research/authors/USWarDept/ORA/OR-S3-V1.html