If you partition the drive, made one partition bootable and restart the Amiga without a floppy disk in the drive it should already try to boot from HDD (either tell you there is not a dos disk in hd0 or show an empty shell window). If this already does not work, you don't need to start any installation. Just go back to HDToolbox and check all your options.
but it doesnt ask where to put it
It does if you choose average or advanced mode. You should *never* choose beginner mode. Not with any software to install. There is no installer script which does everything right without asking the user. So always choose at least average mode.
Bye,
Thomas