Some do an odd install by selecting which drive to boot to via a BIOS menu. But your post is void of details so I can't see what you did different than boot the Linux CD and click on the install.
Bob
I have 2 HDD
I installed windows in 1, linux in the other.
When i boot up in windows, i cant see my other HDD with the linux on it, and vice versa.
How do i fix that?
One HDD is sata ntfs (i think) the other is IDE fat32 (i think)
Also how can I make it so when the computer boots up i can choose which OS to boot into?

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