You've got two options:

(1) Load the whole file into a staging table and do the processing in the database engine, using SSIS to do the final export back out to the second test file; or

(2) Use the transformations provided in the Data Flow to redirect the rows for you. I think a Merge Join and/or a Conditional Split may be what you're looking for, but I usually go for option 1 myself so I'm not all that familiar with those transformations.

John