I have Kubuntu Breezy installed on a Sata hard drive, and it has no problem. The only difference is that the partitions are /dev/sda* instead of /dev/hda*.
On a side note, may I suggest leaving the Windows drive plugged in. Install Kubuntu to the Sata drive, and it will pick up Windows and install a boot loader to the MBR so that you can select Kubuntu or Windows at bootup. Much easier than changing settings in Bios
Also, when you partition your Sata drive, create a FAT32 partition for a shared disk between Linux and Windows. Make the mount point /share, and windows will automatically assign it a drive letter.
I hope this helps