Can I use Time Machine to backup ONLY an external drive?

I am having problems with the internal HD on my iMac and Disk Utility is telling me I need to reformat the drive and restore from backup. Only problem is that my 3TB Lacie Thunderbolt drive I was using for Time Machine recently failed (think it may have happened during an electrical storm brownout). Yep, I know, ***** to be me
The issues with the internal HD are preventing the iMac from booting and I would prefer not to have to purchase various repair software to find one that really works such as Disk Warrior or similar ((despite it getting very good reviews). I suspect it make be HFS corruption but no way to really tell that I am aware of.
I have setup an external drive with Yosemite and booted from that so now my old internal drive is seen as an "external drive".
I am using Disk Utility to make an image copy to a new 3TB external drive I purchased. Writing the DMG is going to take some time.
What I would like to do is to set up Time Machine to backup to a separate external 3TB hard drive (the second one I purchased) and have TM create a backup of ONLY the old internal drive - not the new system as well as the old internal unit.
Is this possible and if so can anyone advise how to do this. Does not seem I can exclude the system drive I am now booted from so that it is not backed up. (This makes sense that TM would be designed this way given its primary purpose is to backup a system).
If TM cannot be configured in this way, is there another option I can use?
Thanks
Andrew

Thanks for that advice. I have heard of it but a friend who does IT support at a University nearby suggested using Disk Utility to save an image - hence this is currently underway at present. Once this is finished I will try Carbon Copy Cloner.
I have another friend who has an older version of CCC - do you know if an old version will work ok or if only the latest supports Yosemite?
Also once I have the clone completed from CCC, is the process then to reformat the old internal drive and then clone from the CCC external drive back to the internal and then reboot and trust all is well?
Appreciate your help Csound1.
Regards
Andrew

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