You didn't state if you will have internet access.
If you will have internet access then I would connect remotely from the iPad.
If you will not have internet access then I would have an iPad version of my app to perform the audit and after the audit is complete I would import the data into the Desktop version, then blank the iPad version.
You can use iTunes or email to place your app on to the iPad.
Filemaker Pro can share up to 9 users.
You may want to investigate the "synch" products offered by SeedCode and 360Works.
You need to maintain a single FileMaker file with 'one record per audit' instead of creating a separate FileMaker file for each audit. You can easily email this file back and forth between your iPad and desktop without changing its name. Remember to close the file on the iPad after each use otherwise you will overwrite the old file in the iPad file directory but still have it open in FileMaker Go app. Create a copy of the file occasionally and append the current date to maintain a number of backups.