:/ There is some confusion in this thread (or I myself am confused). SATA in itself does not work based on Master/Slave principles as far as I know. If I am wrong, please do correct me.
Having multiple PATA drives can be troublesome because each drive has its own controller and each controllers must function while being attached to the same bus. There must be a way to ensure that only one of the two controllers will respond to a command at a time. The ATA standard provides the option of operating on the AT bus with two drives in a "daisy-chained" configuration. The primary drive (drive 0) is called the "Master", and the secondary drive (drive 1) is called the "Slave". You configure a drive to be Master or Slave by altering a jumper setting on the drive or by using a special line in the interface called the Cable Select whereby you would configure the jumpers to operate on Cable Select.
If only one drive is in the PC, that controller responds to all commands from the system. If two drives (and, therefore, two controllers) are installed, both controllers still receive all commands from the system. Each controller must be configured to respond only to commands for itself. One controller must be set as the Master and the other as the Slave. When the system sends a command for a specific drive, the controller on the other drive must remain silent while the selected controller and drive are functioning. Configuring the jumper as Master or Slave enables discrimination between the two controllers by setting a special bit (the DRV bit) in the drive/head register of a command block. No functional difference exists between Master and Slave, except that the drive that’s specified as the Slave will assert a signal called DASP after a system reset informs the Master that a Slave drive is present in the system. The Master drive then watches the drive select line, which it otherwise ignores.
Now, with SATA, each cable has connectors only at each end, and each cable connects the device directly to the host adapter. There aren't any Master/Slave settings because each cable supports only a single device.
What I believe you're trying to figure out, (which is how SNGX answered you, so I assume he thought this way earlier), is whether or not to have your SATA drive ahead of the PATA drive on the boot sequence. Unless you have an operating system on the SATA drive, it's not going to matter whether or not you set it in front of the PATA drive. So, if you want to use your SATA drive as your primary HDD, either reinstall Windows there or clone the data from your PATA drive.