The fat32 will make your life easier in the long run. That guide has everything in it you should need to accomplish the task at hand. I think you will need to use one of the other 2 programs in the guide to clone your drives though. I don't think wbfs manager will see your fat32 drive.
As far as the "first" partition goes, in your disc management screen you should see a list of all of your actual physical drives. Each drive may have more than one partition. The first partition is the one farthest to the left on the given drive. That is the one that needs to be formatted to wbfs if you choose to stick with that method. I understand your confusion on that, I went for a couple days before I realized it myself. Once I understood it I had no idea why it was so difficult for me to figure out.
I think all of the loader will recognize the fat32 format. Depending on what version of the particular loader you are using, you may have to update and possibly change the ios they load from. I am far from an expert on which ones work which way, but will gladly try to figure it out with you if needed.