To begin with...you don't clone a system, you clone partitions. You can clone every partition in that system, but you do it a partition at a time (that's fairly safe).
And you can adjust the size of the partitions with some applications, with free space not being part of the cloned content.
There are lots of programs that allow for cloning of partitions/drives...you need to decide which one you want to use.
The destination is not required to be formatted...all that's required is that there be sufficient unallocated or free space so that the cloned partition can find a home on the drive.
There is no order that I have ever seen required...I select the partition I want cloned, then I select where I want it cloned to...press a button and it begins to happen.
I use Partition Magic 8 for such activities, but there are other programs available (some free) which also enable this activity. The best thing to do is to read up on a few before you try them.
NTFS should always generally be the file system of choice, IMO.