Hardware RAID presents each VD to the OS as separate disks, so unless you choose the wrong "disk" to install to, what you do to one will NOT affect the other - it is the same as reinstalling the OS on one disk of two in a desktop or laptop.
Hi,  I am re installing Windows OS. Our server has PERC 6/i Integrated storage controller witch has couple virtual disks configured. My question is if I format and reinstall OS it won't anyhow effect my storage virtual disks configuration as this is hardware configuration on internal server storage controller? thanks  
OS installation and storage configuration