From my experience, the flat file import task is pretty limited. You could write your own script task or try to find another task.
Here is a list of add-ons for SSIS in codeplex:
http://ssisctc.codeplex.com/
A few catch my eye you should look at:
Regular Expression Flat File Source - A regular expression based flat file parsing source.
Delimited File Reader Source - A source component capable of parsing delimited flat files, including files with rows that are missing column fields.
Delimited File Source - An extremely robust flat file source for Integration Services which handles quoted text and provides full data auditing. Based on the work of Microsoft's Bob Bojanic (Delimited File Reader Source Sample).