Up to you of course, but I'd be tempted to put corepure.gz, corepure64.gz, vmlinuz and vmlinuz64 in (for example) /mnt/sda1/boot, the 32-bit extensions in /mnt/sda1/tce and the 64-bit extensions in /mnt/sda1/tce64
You would then use the tce=UUID="SomeValues"/tce64 boot code to select the 64-bit extensions