Like I wrote: "I suggest you to backup your important files on that external
disk (or another one)". I would use GParted to prepare it.
The farther the backup from the original data, the better. If both are in
the same computer and it catches fire, you lose everything. If both are in
the same house and it catches fire (less probable that the computer catching
fire), you may lose everything. If both are in the same neighborhood and
there is an earthquake (less probable than the house catching fire), you
might lose everything. Do you understand?
Also, do you understand that a backup of the the user data is far more
important than a backup of the system? You can always reinstall a system
(taking a new copy of it). But you cannot recover your family pictures if
they only were on a disk that was damaged. I tell you that because, as far
as I understand (it is not clear), you are talking about "cloning" Windows...
... but you then talk about overwriting it, so I am confused. If you go for
deleting Windows, there is no point in cloning it (install Trisquel in the
space the cloned system would use). You can delete Windows' system
partitions and create in the free space (some of) the three partitions I was
talking about. I was suggesting to use the installer but you can do the same
from GParted if you prefer (during the installation of the "Something else"
type, you then only need to define the two mount points, / and /home).
