What Bootsect.bak Does?

Install Loads BOOTSECT.BAK To Second HDD

during install of Vista ultimate to new system with 2 x 750GB Sata HDD..I partitioned 100GB of the first disk (0) to take the Vista system. Windows asked where to put the installation and I highlighted the new partition but then it indicated it needed space to put what I thought it said was the System Volume? and that there was enough space on the disk 1...now I thought it meant partition 1 and highlighted that and clicked yes in the dialogue window...after the install I saw that it had placed a file of 8kb namely BOOTSECT.BAK onto the second HDD.

In disk management disks show as c: Simple Basic NTFS Healthy (Boot,Page File, Crash Dump, Primary partition) and the second disk as D: simple Basic NTFS Healthy (System, Active,Primary Partition)....Also Both disks show total storage as 698GB each ? Whats going on and can I do anything other than a new install ? If a new install is needed (I havent activated vista yet) what should i do second time around.