The contents of the holding disk have nothing to do with how the client's gnutar/tar/star/dump/whatever decides to handle incremental/full backup decisions, that's up to the client. Gnutar has a special (non-standard) tar format it uses when it's doing --incremental or --listed-incremental backups, and all that magic happens on the client machine. I believe each client will have a directory where the amanda client puts any Gnutar-related file lists. Those stay on the client and don't come back to the server, at least in any of the Amanda versions I've used.
The holding disk is only a temporary storage/staging area for the backup files from your clients. Under normal operations that holding area is empty after a backup has completed. The only reason files would remain there after a backup has completed is that some error occurred with a physical tape drive, the wrong tape was loaded, a client lost its connection to the Amanda server during a backup, or there was more backup data than fits on the tape media. You should never manually delete those files with OS commands like 'rm' because Amanda tracks them and will get confused if they just disappear.
Occasionally, if the Amanda server itself is interrupted during a backup, it can leave partial, incomplete dump files behind, and you should use the amcleanup command to remove them. It will know which files are junk and which are valuable. See the amflush command for sending them out to tape yourself, and see the 'autoflush' setting in the /etc/amanda/amanda.conf file (or advanced.conf if you're on a Debian-ish linux distro.)