Disk geometry (with heads, cylinders and tracks) is something from the age of MFM and RLL. In those days it corresponded to a physical reality. Nowadays, with IDE or SCSI, nobody is interested in what the `real' geometry of a disk is. Indeed, the number of sectors per track is variable - there are more sectors per track close to the outer rim of the disk - so there is no `real' number of sectors per track. Quite the contrary: the IDE command INITIALIZE DRIVE PARAMETERS (91h) serves to tell the disk how many heads and sectors per track it is supposed to have today. It is quite normal to see a large modern disk that has 2 heads report 15 or 16 heads to the BIOS, while the BIOS may again report 255 heads to user software.
For the user it is best to regard a disk as just a linear array of sectors numbered 0, 1, ..., and leave it to the firmware to find out where a given sector lives on the disk. This linear numbering is called LBA.
So now the conceptual picture is the following. DOS, or some boot loader, talks to the BIOS, using (c,h,s) notation. The BIOS converts (c,h,s) to LBA notation using the fake geometry that the user is using. If the disk accepts LBA then this value is used for disk I/O. Otherwise, it is converted back to (c',h',s') using the geometry that the disk uses today, and that is used for disk I/O.
Note that there is a bit of confusion in the use of the expression `LBA': As a term describing disk capabilities it means `Linear Block Addressing' (as opposed to CHS Addressing). As a term in the BIOS Setup, it describes a translation scheme sometimes called `assisted LBA' - see above under ` The 8.4 GB limit '.
Something similar works when the firmware doesn't speak LBA but the BIOS knows about translation. (In the setup this is often indicated as `Large'.) Now the BIOS will present a geometry (C,H,S) to the operating system, and use (C',H',S') while talking to the disk controller. Usually S = S', C = C'/N and H = H'*N, where N is the smallest power of two that will ensure C' <= 1024 (so that least capacity is wasted by the rounding down in C' = C/N). Again, this allows access of up to 8.4 GB (7.8 GiB).
(The third setup option usually is `Normal', where no translation is involved.)
If a BIOS does not know about `Large' or `LBA', then there are software solutions around. Disk Managers like OnTrack or EZ-Drive replace the BIOS disk handling routines by their own. Often this is accomplished by having the disk manager code live in the MBR and subsequent sectors (OnTrack calls this code DDO: Dynamic Drive Overlay), so that it is booted before any other operating system. That is why one may have problems when booting from a floppy when a Disk Manager has been installed.
The effect is more or less the same as with a translating BIOS - but especially when running several different operating systems on the same disk, disk managers can cause a lot of trouble.
Linux does support OnTrack Disk Manager since version 1.3.14, and EZ-Drive since version 1.3.29. Some more details are given below.