Here we will focus mostly on ST and STE machines, but many of written stays for Atari Falcon and TT machines too.

Little history for better understanding:
When Atari ST was launched, in 1985 hard disks were not much used - they were too expensive, exotic pieces of hardware. Standards were not established, and there was no IDE (ATA), later winner in mass storage system for masses :-)   Atari did some support for attaching (in that time yet future) hard disks in form of ACSI port. It was typical for that time: usage of own system, not compatible with any other. But it was not so bad move, considering lack of standards. And ACSI port is actually some kind of simplified SCSI port. After it, some hard disks appeared on market. More success than Atari had independent manufacturers. Typical hard disk kit for Atari ST machines was: ACSI-SCSI adapter and SCSI disk + power supply + driver, partitioner software. In meantime IDE hard disks appeared on market. They were designed to be cheap, simple interfaceable. Atari made support for IDE disks somewhere in 1991-92. Code for boot from such interface/disk is added to TOS 2.06, and latest machines as ST-Book and Falcon had built-in IDE interface.
However, some people did not realised in that time what really happening: I read in some article in German Atari magazine that it is no wise to make IDE interface, because SCSI is just little more expensive, and IDE has no perspective. Now we know that they were wrong. Biggest problem with IDE interface is that it can not be simple connected to machine - you need to open case and solder lot of lines. In case of Mega STs it was little simpler, but still some soldering and mounting connector was required.
Now we have absurd situation that some Atari users have ACSI-SCSI-IDE chain of interfaces.  Main problem here is that Atari bankrupted after 1992, and that there is no expansion port/bus on ST machines.

How it works?
Unlike by modern PCs, there is only very little support for hard disks in TOS. Actually, in TOS is only short code for loading master boot record from hard disks. All further is done by driver and it's loader. TOS has support for FAT16 filesystem - MS DOS compatible. Later TOS versions added some support for bigger FAT16 partitions in form of 'Big sectors'. All that required (compatible) hard disk drivers.

Limitations:
TOS 1.0 was limited to partition sizes of max 16MB due to bug (without big sectors). FAT16 partition has max size of 32MB. FAT16 with big sectors, called BGM may be up to 1GB, depending on TOS version.
ACSI in it's initial form has limit of 1GB for total size of attached hard disk, because of addressing system. It is expanded later in XHDI.
But we should not blame Atari much for those limits. By PC, situation was even worse - max half GB total disk size accessible with CHS addressing by IDE/MFM disks. Not to mention mess in partition tables.
IDE (ATA) went through numerous expansions. Most important is LBA addressing, what accessess hard disks up to 128GB capacity.
BigDOS partitions on PC have limit of 2GB in size, and they are readable on Atari with help of free program BIGDOS + hard disk driver (at least AHDI 3.0 compat.)

Partitioning of hard disks:
In very first sector of every hard disk is partition table. Atari uses so called GEMDOS partition table. It is defined in AHDI. However, we are not forced to use that system at all - because there is nothing in TOS related to it. All is done by hard disk driver. Usage of MS DOS partition system offers as other possibility - it uses same FAT16 partitions as GEMDOS. And we have benefit that such disk will be readable on PC without any special software.

Where we are today (2007) ?
Still some people uses Atari ST machines. Things changed a lot until 80-es of last century. We have now cheap Flash mass storage medias, with low power consumption, fast work. SCSI is developed too, but it is not for mass-market. Nobody manufactures ACSI-SCSI adapters. Ideal would be ACSI-IDE or ACSI-some Flash card interface. But from some reasons they are not available, although there are some projects under development/manufacturing. IDE has advance that CD ROM/DVDs can be attached too.
Problem is that ACSI and IDE (ATA) are not compatible. For instance IDE has 16-bit data bus, while ACSI 8 . Even bigger problem is control: ACSI first gives command code, then parameters, while IDE does it in opposite order. So, designing ACSI-IDE IF is not so simple.

There is still a lot of working, good quality ACSI-SCSI adapters used with Atari machines, and they are best supported by  software. IDE is not so good supported, and most of drivers is obsolete.
Problem is when someone wants to buy adapter and mass storage media: what to buy today?
May go to E-bay and look for some second-hand combination. Prices are not to good, considering that new Flash card of 4GB costs under 50 Euros, and will be gradually cheaper.
Or waiting...

P. Putnik ,  March 2007.