You can always choose a custom install option and choose the partition that Windows is installed on. The only caveat is that Windows boot loader will override IBM/Lenovo's boot loader such that the service partition is no longer bootable. There are two ways around this that I am aware of. Use Lenovo's Rescue and Recovery - Recovery repair media
[diskette] to repair the MBR or boot a recovery media CD to access the service partition. You have to burn your own recovery media CD using a ThinkVantage menu choice.
It seems it should be possible to use EasyBCD
to edit the boot entry of the Windows boot loader and add the service partition as a boot choice after reinstalling Vista. I haven't read that anyone has done this though. You could use EasyBCD to see what is currently in Windows boot loader.
See also: How to automatically repair Windows Vista using Startup Repair