No, the FMC is not responsible for Automated Manifest Filings (also commonly referred to as AMS filings) and SCAC codes for Vessel-Operating Common Carriers. 

U.S. Customs and Border Protection (CBP) is in charge of Automated Manifest Filings. You must file Automated Manifest filings with CBP. A list of vendors that can assist with AMS filings is published by CBP here

The National Motor Freight Trade Association (NMFTA)  issues Standard Carrier Alpha Code (SCAC) codes. You can apply for a SCAC code through the NMFTA here.