There are several ways you can do this. The way I usually do this is to FTP the file down to a working directory, and then use a ForEach Loop to process the file (or files, if more than one) from that working directory. Once the file is processed, you can use a File System Task to move the file from the working directory to an archive directory.
Feel free to post more info if this won't solve your problem.
hth,
Tim
Tim Mitchell, Microsoft Data Platform MVP
Data Warehouse and ETL Consultant
TimMitchell.net | @Tim_Mitchell | Tyleris.com
ETL Best Practices