When starting a fresh installation you should try with standard BIOS options. If something doesn't work you should try to modify BIOS options. For example a well known trouble maker is the Plug-and-Play - PnP option (which comes with different names). See also the BIOS section in the hardware section below.
There are many boot options, which have effects on the behavior of laptops, e.g. apm=on|off and acpi=on|off: For details see BootPrompt-HOWTO and the Kernel documentation in /usr/src/linux/Documentation/kernel-parameters.txt .
Partitioning can be done in a very sophisticated way. Currently I have only some first thoughts. I assume that with laptops there are still some reasons (e.g. updating the firmware of PCMCIA cards and BIOS) to share Linux and Windows9x/NT. Depending on your needs and the features of your laptop you could create the following partitions:
BIOS, some current BIOSes use a separate partition, for instance COMPAQ notebooks
suspend to disk, some laptops support this feature
swap space Linux
swap space Windows9x/NT
Linux /home for personal data (please consider an encrypted partition for security reasons, for details about encryption see the according chapter below)
common data between Linux and Windows9x/NT
small (~32MB) boot partition for yaBoot (Linux/PPC boot loader), in HFS MacOS Standard format.
Note this chapter isn't exhausting yet. Please read the appropriate HOWTOs first, e.g. the Partition-HOWTO .