Hard drive Issues

[preyed]

I formatted today and I noticed that when selecting which drive to reinstall windows 7 on, both of my drives were listed as primary system drives, I have two drives, one is OS (System Drive) and the other is storage. Also the storage drive was above the normal drive I use for system. Normally, the storage is listed below. Alright so I just ignore it and contiune to install and once I got into windows I noticed that my storage drive wasn't listed in My Computer. I had to actually goto Disk Management and assign it a drive letter. While in there, I noticed that my System drive is now Labled as Disk 1 and the Storage Drive is Disk 0. So, I got that all set and I started installing software again and I noticed that windows is silently installing bits and pieces onto my Storage drive as if it was the primary drive.

So my question is, how to set it back to way I had it, Primary drive as System/Primary Partition and the Secondary drive as a pure file holder?