They can be wav, syx or ir.
The easiest way to send when tweaking is to use Cablab and the scratchpad as it's a great way to audition. You can then send it to a specific cab slot, export it or save the session. AxeEdit and FractalBot will also send IR's to the AxeFXII. Basically for mixing I use Cablab and if I'm just dumping IR's in there I use the Cab Tool in AxeEdit. I don't bother with FractalBot for anything but firmware and backing up/restoring banks.
It sends it in syx.
It is not the case so you are fine.