Think of the BIOS settings as a roadmap, index, or directory that the operating system uses to find and access the system hardware.
Both the BIOS code, and the settings you adjust create an index of the hardware and firmware services installed inthe PC.
As to your specific questions;
For the FDC, the BIOS settings are used like switches to turn the FDC on and off, and to set the mode of operation.
SMART has to be in both the motherboard and hard drive controller BIOS's for it to operate.
LPT: Again, the BIOS settings act like switches to enable and structure the port and supported modes.
Hope this helps.
There is general information available for download at most of the BIOS mfg web sites. (AMI, Award, Phoenix)
You might also check out www.wimsbios.com for more information.