The Claris Emailer installer was designed for floppy disks (3 of them) and so your installer should have come with three folders labled "Disk 1", "Disk 2", and "Disk 3". You should be able to copy those folders directly onto floppy disks for storage.
If you want real executable install floppies, you must name the disks as above (no quotes) and then copy the "contents" of the disks (not the folders saying "disk 1", etc.) onto those disks. If you do all that, you should be able to run the installer directly from the floppies.