Drive letters assignment during boot up

I have a simple question:
How are the drive letters assigned to the different hard drives and paritions, respectivley, during the boot process. Is this determined by the BIOS or the Master Boot Record or …, and which drives/partitions take precedence when a decision is made. I am having a problem because my drive letters change when adding a second HDD to a system, and I cannot boot normally into a multiboot system. I am curious if there is a way to change the way letters are assigned to logical drives. Windows 2000 takes care of the problem (although in a really strange way), but Windows 98 cannot find the partition where its sytem files reside bacause there resides the primary partition of the second hard drive.

Thanks!