Most BIOSes have an entry in the Standard Setup menu for each of the four IDE/ATA devices supported in a modern system (primary master, primary slave, secondary master, and secondary slave).
For each one, you can enter a value for each setting in this section (type, size, cylinders, etc.) See here for details on hard disk geometries and data structures.
It should be noted that all modern hard disks use special technologies that makes simple geometry figures like "cylinders, heads, sectors" inapplicable. For example, almost all modern drives use a variable number of sectors, and are set up using an "approximate" figure in the system BIOS. This isn't something you generally need to worry about as you set up your hard disk, but remember that if it says "63 sectors" that doesn't necessarily mean the drive really has that number in each cylinder. In fact, it normally will not.

in some detail in the section on hard disk geometry.

Virtually all BIOSes now come with IDE device autodetection. This comes in two forms:

• Dynamic IDE Autodetection: This is the fully automatic mode. You set one or more of the IDE devices (primary master, primary slave, etc.) on "Auto" and the BIOS will automatically re-detect and set the correct options for the drive each time you boot the PC. The BIOS will usually display on the screen what device it finds each time it autodetects. For most people, this is the best way to go; it ensures that your BIOS always has the correct information about your hardware, and it removes any possibility of you installing a new drive but forgetting to set up the CMOS properly, or of changing a parameter by mistake in the setup program. Not all BIOSes offer this setting but most newer ones do.
• Manual IDE Autodetection: This type of autodetection is run from the BIOS setup program. You select autodetection, and the BIOS will scan the IDE channels, and set the IDE parameters based on the devices it finds. When you save the BIOS settings, they are recorded permanently. The disadvantage of this is that if you change devices, you must return to the BIOS to re-autodetect the new devices (unlike the dynamic autodetection scheme, which does a fresh autodetection each time you boot the PC). Virtually every BIOS created in the last 8 to 10 years offers manual autodetection.

When you use dynamic autodetection, the BIOS will normally "lock" the individual device settings that are being automatically set by the BIOS at boot time. Most systems that provide manual autodetection will not lock the individual settings; they autodetect, set the settings, and then let you change them if you want to.
In most cases of course, you will not want to change what the BIOS detects.

Most BIOSes that allow dynamic autodetection also allow manual autodetection. The choice is yours. Using some sort of autodetection for IDE/ATA devices is strongly recommended. It is the best way to reduce the chances of disk errors due to incorrect BIOS settings. It also provides immediate feedback of problems. If you can't autodetect a drive from the BIOS, you know you have a problem even before you try to boot up.

Note: On most BIOSes, you perform a manual IDE autodetection using a special entry with that name on the BIOS setup program menu. This entry autodetects all IDE/ATA devices, one at a time. However, other BIOSes "hide" autodetection.
For example, on some BIOSes you autodetect an IDE/ATA device by moving to the "Type" setting for the device and hitting {Enter}. This runs the autodetection for that device only. Check your manual if you are having problems finding the autodetection facility.

Warning: If your BIOS contains a "hard disk utility" or "low-level format" type program, do not use it on IDE/ATA drives. These utilities are intended for older MFM and RLL type devices. Modern IDE drives do not need low-level formatting, interleave factor settings, or media analysis under all but the very most unusual circumstances, and when they do need it, they need special utilities specially designed for the type of drive you are using.