A: The option to allow disks with more than 1024 cylinders, which the AHA1542C card can recognize, is only required as a workaround for a PC-compatible BIOS misfeature and should be turned off under Linux. For older Linux kernels you need to turn off most of the advanced BIOS options all but the one about scanning the bus for bootable devices.
A: If your disk is an IDE or EIDE drive, you should read the file /usr/src/linux/drivers/block/README.ide (part of the Linux kernel source code). This README contains many helpful hints about IDE drives. Many modern IDE controllers do translation between "physical" cylinders/heads/sectors, and "logical" ones.
SCSI disks are accessed by linear block numbers. The BIOS invents some "logical" cylinder/head/sector fiction to support DOS.
Older IBM PC-compatible BIOS's will usually not be able to access partitions which extend beyond 1024 logical cylinders, and will make booting a Linux kernel from such partitions using LILO problematic at best.
You can still use such partitions for Linux or other operating systems that access the controller directly.
It's recommend that you create at least one Linux partition entirely under the 1024 logical cylinder limit, and boot from that. The other partitions will then be okay.
Also there seems to be a bit of trouble with the newer Ultra-DMA drives. I haven't gotten the straight scoop on thembut they are becoming a very common problem at the SVLUG installfests. When you can get 8 to 12 Gig drives for $200 to $300 it's no wonder.