Update existing SQL Server 2008 table via Flat File using SSIS
You can follow either of the below approach :


Load the entire flatfile into a staging table and then update / insert the records based on the criteria you want. After the process is completed, you can truncate the staging table.
Look into using Lookup transform as described in Updating Rows in Incremental Loads – Level 4 of the Stairway to Integration Services


Refer to this excellent series : Stairway to Integration Services for more details.