As Piru already said, DMS, TransADF and such tools just reading the tracks in standart OS way won't be able to read those copyprotected disks. :-(
You'll probably see the protected tracks marked as bad or unreadable.
To be able to create backups of them i wouls suggest you to use WWarp (part of WHDLoad) @
http://www.whdload.deBut you need a HD to save the disk images, and they're mostly more than 1MB reaching 4MB or 5MB sometimes!
WWarp can compress them with XPK though to save diskspace. And you'll be able to write them back on standart floppy disks again with WWarp.
Or contact the CAPS Team, they'll send you a tool to make images of the disks (nearly same way WWarp does) and save them on HD, but this one won't use any compressing so be warned if you have no HD space left.
Then send those images created with CAPS tool to the CAPS Team, they will analyze them if they're really good original copies of the game or just a simple cracked version. After that's done, and if they're truly originals, they'll convert it to a usefull image format which can be used with WinUAE!!!
So that's preserved for the future. I've already participated with all my original games i've got. :-)
Btw, check their site to see if your games are already imaged (backed up) or not.
CAPS:
http://www.caps-project.org/