what you are saying doesn't mean anything.
I'll make some global steps describing the process.
Tell me up to where you are following. which point you don't understand.
What I understand :
1. You have 2 different HDD.
HDD1 (with your Wii games), and HDD2 (you want two partitions in this one, one in FAT32 for Wii and Gamecube, and one in NTFS for PC Movies).
2. You want to transfer the Wii games located on HDD1 into HDD2
3. You want to know if you need to copy all the files one by one, or ... of course all the files need to be copied.
When you copy multiples files from one folder to another, are you not selected all the files -> copy -> select destination -> paste (or drag and drop), it's done in "one user's input" but all files are copied one by one in that process.
You are not making multiple drag and drop, or copy/paste, but the files are copied one by one.
For the wii, it's the same thing. You use a manager, you mount your two different HDD, you select all your games from HDD1 -> Copy to HDD2 -> one click but all file will be copied one by one.
What you will need to do:
1. partition your HDD2 (ATTENTION, IT WILL DELETE EVERYTHING ON THE DRIVE)
you can use Windows HDD manager, or any partitioning tools like "Easus".
1.1 Delete all partition from HDD2
1.2 Create a new partition, select the size you want, it must have these options : Primary, active, FAT32, 32k cluster size.
1.3 Create a new partition, select the remaining size. It must have these options : Primary, NTFS, auto (for the cluster size)*
* Alternatively, for the second partition you can choose an "extended partition" instead of primary. inside the extended partition, you can create Logical partition.
HDD can have only 4 partitions. (primary or extended). Extended partition can hold multiple logical partition. this option is used if you want more than 4 partition in your drive.
If you want only FAT32 and NTFS, (2 partitions), you can use 2 primary partitions.
2. Copy the games from one HDD to another
2.1 Connect both HDD to your computer
2.2 Launch Wii backup Manager
2.3 in "Drive1" tab, select the HDD1 with the Wii games
2.4 in "Drive2" tab, select the HDD2 FAT32 partition drive's letter
2.5 Go back in "Drive1" tab, choose "Select" > "All"
2.6 choose "Transfer" > "Drive2"
All games located on Drive1 will be copied to Drive2
Done.