Setting the jumper on an IDE HDD to "Master" does NOT have anything to do with determining the boot device. Master and Slave are ONLY ways to identify two different devices one ONE IDE port.
In your BIOS Setup screens you can find a place where you specify the Boot Priority Sequence. All of the drive devices in your machine will be listed there - floppy drives, optical drives, and hard drives, maybe even a USB flash drive if your mobo supports that. YOU set which device is tried first, which second, etc. And YOU set here how many different devices will be tried before quitting. Most people set it so an optical drive is the first device tried, then the particular HDD that you know has your OS on it, and no other devices in the list. Among your hard drives, the Master device on your IDE port and the other unit you connect (via adapter) to a SATA port both will be shown, and you can choose to use ONLY the one on the IDE port as a boot device.