Within the Site Settings (Settings -> Status -> Log Import Status) you will find the status of all imported logs.  This will provide you with the file names as well as the status of importing and date information.  In a case such as yours, the file name should reference the individual folder where the file is located.  SmarterStats has the ability to handle load balanced sites with a setup such as yours.  If you notice that either the files aren't being imported properly or the data doesn't look to be correct, a support ticket would be needed though for our support team to take a further look.