Well I can probably answer some of your questions.
1) You can probably just transfer your saved game files from the HD to a flash drive and then back to the HD after you have re-formatted the HD (I'm assuming that is what your doing).
2) In order to reuse the HD's, I usually just format them and install them after you have your system up and running on the new hard or freshly formatted HD. This way the drive space available is at its maximum size for your use (no OS on them or other items that you won't need).
3) It doesn't matter which HD you put the OS on, but if it were me, I would put it on the fastest HD that you have (which I'm betting the 500 gb is, since I haven't seen a 150 gb HD in a while for sale).
Yes, you can just transfer your files to a drive and then back to the filesystem. You can also copy your "steamapps/common" folder to not have to re-download all of your steam games.
All you have to do to reuse the parts is plug them in, and install windows like normally, formatting/deleting any existing partition when you do so. Any guide that shows you how to install windows should show you how to do this.
I would personally install the operating system to the 500GB hard drive... unless the 150GB hard drive is a SSD, not a hard drive. The reasoning behind that is that nobody makes 150GB hard drives anymore, which means it's old and more likely to fail - thus I'd want my operating system on the 500GB hard drive with unimportant things like game installs on the 150GB hard drive.