The port closest to the edge of the console is the one d2x expects the drive to be in. One problem with that guide, though, is that it recommends installing d2x beta53 as IOS249[56] and beta52 as IOS250[57]. You shouldn't do that. Use beta52 for both slots. You can just redo it and install beta52 over the top of the other one if you want.
You can just use one FAT32 partition for everything. Wii Backup Manager can split files so they fit when it copies them.
1. Alright fantastic, I'll keep the USB HDD plugged into the bottom port / closest to the edge, glad to know its normal.
2. OK, no problems, I can change them to both use beta52, shouldn't be a problem.
3. I'm guessing I shouldn't try 'updating my wii' when I make a new network connection? What happens is, I use the USB Network Adapter for the Wii (WiFI doesn't reach), so I had to remove the wired connection from the main menu, whilst I was mucking around trying to work out which USB port to plug the HDD in. So every time I made a new connection it would pop up saying to update. I probably should of checked if the Wii needing updating before doing steps 1 to 5 (it was on 4.3)? Or is there actually an update that I should do / have done?
4. So installing App into the homebrew channel is basically 'not really installing, but copy/pasting the program into the apps folder' correct? I think that confused me a little at the start but I think I might also try USB Loader GX, I can have both WiiFlow and GX right?
5. WiiFlow 4 The Masterpiece Pack by Abz - I believe this is more updated/more features compared to the default WiiFlow (which I grabbed from the net). Only thing is, I have no idea how to install it or get it running, are you just suppose to copy/paste the entire structure/files into the main directory? If so, then all I need to do is remove my current WiiFlow directory from the apps folder correct?
6. I would prefer to keep the files in ISO format, that's why I wanted to use NTFS (>4GB limit) but I could just use one main FAT32 partition. It seems to be working with split partition (one as FAT32, one as NTFS) so I might just leave it this way for the time being, because from memory I did try Dolphin ages ago and it used ISO files, I can't remember if it ran WBFS files? But yeah when I use Wii Backup Manager then transfer to external HDD, it converts the ISO to WBFS so something to think about I guess, unless I don't use it and just copy/paste the iso into the wbfs folder, but I'm not sure if that works?
Once again, thanks for the help