Yeah, go for one partition, also don't worry about the split just use Wii Backup Manager to transfer the games as wbfs format, I too was worried at first that I might get slowdowns or any issues but nope, it runs just as if it's one big file, goes back and fourth with no problems (now if only PS3 did the same but nope, you still need to transfer the entire game to the internal HDD there).I will give that a shot. 1 partition sounds good at this point!
Did you have to set the partition as "active"? I see some posts referring to that..
As for your second question, afaik you don't really need to set it as primary, I never done it before and it works great for me, the brand of the hard drive seems to matter though so I recommend WD from my testing.
I never heard of such a thing, I'm planning on getting a 2TB WD HDD soon "still on 1TB but am running out of space" should I transfer my GC collection first or does it not matter?I have a 4TB WD MyBook also. I originally thought the same thing as you and tried to do 2 drives connected at the same time and it was just too confusing for me to figure out and get working right. I thought the drives had to be formatted to 32k cluster size but no matter what I did I couldn't get my 4TB drive to do anything less than 64k. So I formatted the whole thing to FAT32 with 64k clusters and put everything onto one drive and everything works great for me.