to use USB Port1, you need compatible IOS :
- hermes cIOS v4 or v5.x
- d2x v9 beta
- d2x v10-alt
- IOS58
Then, setting "USB Port: both" and "multi partition : enabled" should be enough to mount both drives and list all partitions at the same time.
Did you try to user "USB Port : 1" (or 0). one at a time instead of "both" ?
when you change the USB Port, select the default partition to list (in case show multiple partition option is disabled) or the one to use to install games from disc.
Attention, if your drives have different partition numbers, or different folder setup, your settings might be broken as few paths will not point to the correct location anymore.
Please let me know if your drive are detected independently.
Another thing to know if you want to use dual partition is that Nintendont is using IOS58, and nintendont will mount the FIRST hdd it finds and the FIRST compatible partition from that HDD.
the issue is that IOS58 is mounting USBPort1 first, then USBport0. cIOS are mounting the drives in the other order, so if you plug the Gamecube HDD on port0 USBLoaderGX will see the games but nintendont will not access it, it will try to mount the gamecube iso from Port1 and will not find the file.
So, you need to connect drives in this order :
USB port 0 : Wii HDD
USB Port 1 : GC HDD
but when doing this, I think (I'm not sure!) you shouldn't set USBLoaderGX to use IOS58 inside the loader or it will also mount the drives and partition in reverse order, which means the gamecube games will be on usb1:/games/ (first mounted partition) and Wii games on usb2:/wbfs/ (second mounted partition).
When the loader will reload to cIOS and tell the cIOS to load the game on usb2:/wbfs/ that partition number will not match anymore as cIOS are mounting the partition in incrementing order and will expect the games on usb1:/wbfs/ instead.
Using a cIOS in USBLoaderGX should be fine, as it sends the path to the gamecube game without the partition number to nintendont, and sends the correct partition number to cIOS for wii games.
Setting a dual HDD setup is a little hard due to that init order difference.