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Doesn't applying the builder image completely wipe the hard disks?

Yeah, which is why you leave the old disk unplugged while the builder does your new one. Then you can use the new disk as the master, and the old one as the slave.

The player doesn't care, as long as the player software is loaded onto the master.

I understood that much, but I've been reading things very specifically in this process, and I was mainly focusing on the part where he said "building both drives with the builder image." That would lose all the data, I said so, and he then said I wouldn't. I just wanted to be crystal clear on it

I did format the new drive in that way, so when I get the jumpers I may arrange them just like you said. That sounds fine.