You can boot from a device on primary or secondary IDE ports. If you have A hard drive and you do not use cable select and you use the Master jumper on the back of the hard drive it will be the master even if it is in the secondary position on the cable. Just dont have 2 drives with both master or both slave jumpers set, on the same IDE Cable, or you will probably not be able to use either.
When you partition a hard drive you have to mark the partition as bootable. If you do not, even if it is formatted with an operating sysem it will not boot. Sometimes FDISK does this automatically on a one hard drive system with no extended partition, or drives not split up into multiple logical drives. With multiple hard drives or logical drives, you have to select which partition/logical drive/hard drive is the bootable partition.
If you have 2 hard drives, I recommend unplugging the cables on the one with the data you do not want to destroy! It is easy to erase the partition on a good hard drive by mistake. If you do delete a partition.
You can not boot from a hard drive if it has never been formatted or does not have a partition. There is no file system on the drive to read, so it can not load an OS. Change the boot order to read the floppy and/or the CDROM and use the software supplied by your OS or hard drive manufacturer to setup, partition and format the hard drive.
The CMOS/BIOS sets up the drive to make it addressable. Most newer motherboards do this automatically. This involves setting up the sectors, heads, cylinders, etc. It also involves what drive to boot up. It is completely separate form a FAT table or the MBR. Most drives today have an initial Master Boot Record set up so the drive can be formatted. Still some software has to be used to partition and format them.
If you look for the appropriate forum for the operating system, such as win95/98 or NT or XP they may have some additional infomation or a hard drive FAQ.
If you tell it to boot from the CD and it cant find it or there is no disk and there is no other optional source to boot from often the boot just hangs. Often this is due to 2 drives both set to MASTER on their jumpers on the same IDE cable. Sometimes you can hit ctrl or some other key to get the sytem to boot from the CDROM.
If you do not like my post feel free to point out your opinion or my errors.