If the FBI is conducting an investigation into possible criminal activity by Carrier IQ then the manuals and guides are direct evidence showing what the company intended the software to do, making it evidence in an ongoing investigation.
Not discounting the possibility of that (I specifically stated it in the article), but I'd bet even odds FBI has some knowledge of accessing Carrier IQ data.
The FBI have professional phone forensics/evidence labs around the country. They work with handset manufacturers and special purpose vendors to extract and analyze every bit of data that exists in the phone.
It's inconceivable that CarrierIQ would store unencrypted data on a large number of phones and the FBI would not know how to access it. More than likely, CIQ sells them the tool to do it, or at least provides documentation.
