My understanding of what happens when using separate drives is that one drive is given priority in the BIOS/UEFI menu and then people just use the device menu when using the secondary drive. Windows really only cares about its own drive with this setup, so the bootloader on the other drive is safe. I’ve never actually done this myself since the only system I dual boot on is my laptop and it only has one drive installed. To answer your second question, I just use my bootloader (GRUB in my case) to select which OS I boot into.

Some people recommend having Linux and Windows on entirely separate drives since Windows doesn’t always like to play nicely with Linux. The only issue I’ve ever had with them on the same drive was the time Windows ate my bootloader when upgrading from Vista to 7. Another thing is that you should install Windows first because it will eat the bootloader (as previously mentioned) if Linux is installed first. I also recommend keeping a flash drive with System Rescue CD installed handy in case you have to repair the bootloader.

Edit: Typo

For anyone not familiar with it, the Tenerife disaster is the deadliest aviation accident of all time. A quick summary is that 583 people were killed when two Boeing 747s collided on the runway at Los Rodeos Airport.

Thank you for letting me know. I wasn’t aware since I’ve only every used it on Linux.

I wouldn’t recommend Clementine since it’s unmaintained. You might want to consider Strawberry instead, which is an updated fork of Clementine.

That having been said, I actually use Audacious because I like using old WinAmp skins.

This is what I do with my mom and her boyfriend. I’ve had them on Linux for a few years now and neither have managed to break anything.

In Yakuake’s settings.

I had to set the transparency in individual color schemes to get a transparent background.