but still Win32DiskImager or Etcher will copy the whole thing,
independent how many partitions are on the card... a 8GB SD card will give a 8GB file.
for storage you can zip it down.
but you might have problems restore it to a other card because
even if nominal same SIZE, if some MB missing restore will fail.
to avoid that there is a way to shrink the partition little bit.
the best backup of SD cards is a copy by
RASPBIAN / desktop menu / accessories / SD card copier
( means not need a PC, but use the USB card reader connect to RPI )
because it can even copy to smaller cards / as long the content fits /
by the way: it can also copy to a USB stick ( instead of SD card in card reader )
and if RPI3 has OTP USB boot enable! / or any RPI have ( a small) SD card with bootcode.bin file only /
you could ( after copy ) boot from that USB stick by
/ power OFF / remove SD card / power ON /
StephenBartel wrote:So which one should I choose to clone? The boot partition or the other partition?
you need anyway both!