You can find many boot managers on the web, some free such as GAG booter. In almost all cases, you can swap the boot drive in the boot manager and hide the other drive (and / or windows OS on the other drive.) In my experience this often, but not always works. In the cases where it does not work, it is necessary to alter the boot order of the drives in the bios before each alternation of the two systems. This typically is where one drive is SATA and the other is IDE.
In neither case mentioned above (software change or bios change of booting drive), is there any need to worry about master and slave settings.
One pitfall to avoid is having the first-installed windows system 'visible' when installing the second. That way, you will likely run into various strange problems like finding your 2nd copy installing itself as drive X: where X: can be almost anything. In short, before installing the second copy, be sure to run FDISK or a similar partition manager such as gparted, to mark the first install as 'hidden'. The boot manager you decide to use will do the job of unhiding it to use it when required.
