RAID Server, logical drives/partitions

I received a new server with a RAID controller and 5 SCSI HDD.
I want to put the first two HDDs in an array with RAID1 and three HDDs in a second array with RAID5.
My question;
What is the best way to define the logical drives/partitions?
1. At the RAID level.
2. At the OS level (WinNT4.0).
Please explain your opinion!
Thank you.