|If the second hard drive is the 'slower' one and is does not contain your operating system then it cannot slow down your boot time.|
In order to give you details about setting your BIOS settings, we need your motherboard make and model number, or if it is a factory built system, then we need the make and model of the system. This information is downloadable in your manual.
Slow boot times are most often caused by 1- too many programs loading with Windows, and 2- your hard disk is too fragmented.
To fix #1, Run msconfig and go to the Start Tab and uncheck all except Microsoft and your antivirus program, Apply and restart the machine.
To fix #2, start your Disk Defragmenter and run it.
Another thing that may slow down your booting is if you are running a 'heavy' avtivirus program like Norton or McAfee which are often referred to here as 'Bloatware' because they waste system resources. If you have one of these, consider uninstalling it and going to the Free version of Avast instead. In order to completely remove either of these two completely (so they will not continue to slow you down) you need to download their uninstaller from their website.
Another possibility is that you do not have enough memory (RAM) for your operating system, For 32bit Vista, you should have at least 2GB of memory installed.
You have to be a little bit crazy to keep you from going insane.