ukadam,
do not activate the partition. MS assumes that the "activated" partition is the one to boot from. Using DiskManager, format the drive.
You might not be pleased with the drive letter that Windows assigned to your harddrive.
Personally, I use diskmanagement to assign the letter M to my DVD drive to "get it out of the way". Then remove any usb sticks or drives, and using DiskManagement change the drive letter for your second drive to the letter you desire.
Oh yes, I don't have a second hard drive handy but quite often using DiskPart you can mark a partition on your second drive as active without any problems.
Other tricks to play if this is a desktop is to simply disconnect your main drive and then using your Windows 7 DVD, shift+F10 to get to a command prompt and then using diskpart to set up that second drive. AFter that is finished, and with power off, reconnect your main drive. Now when Windows 7 boots up there will be no complaints.