I was looking for a way to do this as well with AWStats but couldn't find one.
As a work-around, I'm using a utility called Log Parser from Microsoft to split my IIS logs based on the web directory found in the cs-uri-stem field of the IIS Log Entries. There's a feature called Multiplexing within this utilty that I'm using to write separate log files to a windows directory that is named the same as the web directory found in each IIS log entry. (Log Parser is a suprisingly cool utility that allows a variety of different log files to be parsed using SQL-like query language.)
I then turn AWStats loose on each directory to get the directory specific information.
Brute force, not easy or elegant, but it seems to be working OK.