You can change the settings for where the Laserfiche server writes audit data in the Auditing node of the Administration Console, the relevant settings are "Audit file location" and "Rollover directory".  These are per-repository settings, so you need to do it for each one.

That will cause LFS to write to the new location, but existing audit logs will stay put.  You'll need to manually move those from their current location to the new one.  You'll want to delete them from the "Rollover Logs" node, otherwise LFS will advertise to Audit Trail that it possesses audit data that it does not.

When you set up Audit Trail, you'll point it to the repositories and you'll point it to the folder(s) containing the old logs you copied.  Do not point it to the active rollover folder, Audit Trail gets confused when it sees the same audit data available from multiple sources (LFS and the file system).