boot2 is where BootMii is installed to. It can also be installed as an IOS, but to safely restore a NAND dump, it is strongly advised that you only do it if BootMii is installed as boot2 (but this is not possible on newer Wiis, hence the IOS option exists at all).
If BootMii appears when you turn on your Wii, its installed to boot2. If it doesn't, and you haven't changed the autoboot settings, it is installed to IOS and you shouldn't attempt to restore a NAND dump with it.
As for running bootmini.elf: I believe you can just place it anywhere on the SD card, and you can browse to it with the browser in BootMii. For simplicity it may be best to put it in the root of the card.
If it doesn't work this way (commonly there is a green or blue screen instead of it running correctly), rename it to "ppcboot.elf" and put it in the "BootMii" folder on your SD card, and it will autorun when you turn on your Wii. (Make sure to back up the old "ppcboot.elf" beforehand and restore it afterwards).
Any WAD of HBC is completely illegal. You could use ShowMiiWads to extract one from your original NAND dump and install it into the new NAND with ohneswanzenegger, but then you would most likely get a scam warning every time you load it. (I believe reinstalling it with HackMii Installer booted via HBC would fix it, but this way seems a lot more complicated to me).
If BootMii appears when you turn on your Wii, its installed to boot2. If it doesn't, and you haven't changed the autoboot settings, it is installed to IOS and you shouldn't attempt to restore a NAND dump with it.
As for running bootmini.elf: I believe you can just place it anywhere on the SD card, and you can browse to it with the browser in BootMii. For simplicity it may be best to put it in the root of the card.
If it doesn't work this way (commonly there is a green or blue screen instead of it running correctly), rename it to "ppcboot.elf" and put it in the "BootMii" folder on your SD card, and it will autorun when you turn on your Wii. (Make sure to back up the old "ppcboot.elf" beforehand and restore it afterwards).
Any WAD of HBC is completely illegal. You could use ShowMiiWads to extract one from your original NAND dump and install it into the new NAND with ohneswanzenegger, but then you would most likely get a scam warning every time you load it. (I believe reinstalling it with HackMii Installer booted via HBC would fix it, but this way seems a lot more complicated to me).