A HARD DRIVE QUESTION?

Safe boot should be disable-able from the BIOS. As far as your linux distro is concerned what I would do is install the hard drive with the linux partition and set it as the primary boot drive (in BIOS), then what I would do is from within that linux run 'sudo grub-install /dev/sda' to reinstall the bootloader on the master boot record of your Linux drive. It should then detect the Windows install and add it to the bootloader's list. The bonus of doing it this way is a near zero chance of mucking up your windows bootloader in case you ever decide to scrap the linux install (just set the windows drive as the primary boot device in BIOS and you're done)

yes and no

yes you can use it as secondary, no you cant boot it because the win 7 installation is set to fit to the EMachine and wont work correctly on the other desktop. what you have to do is format the other HD thats on the emachine and the take off or unplug the HD with linux, connect the other HD and install windows. once that is done, connect both of them and go into the biod and make sure that the first bootable HD is the one that has linux installed. after that, GRUB (linux bootloader) will either find the OS on the HD or just proceed as it usually does. if it doesnt show anything, you will have to reinstall grub or reconfigure it yourself if you are a badass like that. but you can reinstall it with a linux live cd (preferable). follow these instructions for that - http://www.youtube.com/watch?v=ajs9rO5upZA

once that is done, re ensure that the linux HD is set to boot first! after that, if everything went well, both linux and windows options will appear in GRUB :) - Good Luck!

yes it will work i have 3 hdds on my gamerig one has linux 2nd has win7 and 3rd has win8