does your cd rom show up in the bios? if so as was said earlier you should boot from the cdrom first then the hdd second the floppy third.
from there the disk takes over and will format the drive putting on a partition. then it will load on the files to install the os then it will install the application asking you to confirm details and the cd key number.
i dont understand your sentence "But when i plug in the hdd that has been formatted in, it doesnt like that fact its got nothing on it and it will just not boot from cd..." is this an external disk?
Make sure the floppy disc ribbon cable is inserted the right way round and see if it is detected in the BIOS then.If not load the default BIOS settings/clear the CMOS by using the jumper near the battery (or removing the battery) and try again.