Yes, you'd need partitions for that.
Can FDISK see the USB drive? If it can, you should be able to partition it using that. If not, one option is to take it out of the caddy and connect it to a laptop (it being a 2½ inch drive) which you boot with a floppy containing FDISK.
If I read your question right (and I'm good at getting the question wrong!), your confusion is about primary, extended, and logical partitions.
Primary is usually the first partition on a drive, and is one you can "boot" from. Different systems limit you to how many of those you can have - anything from one to four, in my experience.
Extended is the rest of the hard drive. You need only one extended partition, using all the rest of the drive that isn't primary. You then break that extended partition down into as many as you like...
Logical partitions. They are actually like subfolders within the extended partition, but if you treat them as separate partitions, they will go along with that.
Changing partitions tends to wipe off everything that's on the drive (not necessarily, but that's the way to work - if you need to preserve stuff, then use Partition Magic or one of the Windows equivalents. Linux stuff is much more accommodating in that respect).
So, my suggestion would be:
1. Decide how many partitions you want (sounds like 4).
2. Create one 25GB primary partition.
3. Create one 75GB ("all the rest of the disk space") extended partition.
4. Create three 25GB logical partitions in the extended (the last one might be a tad more or less than 25GB).
5. Format all those partitions (might take a time).
7. Continue as planned with the clone software - whichever package you've chosen to use.