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in the past I have dual booted Windows and Ubuntu however it was always a huge mess that I felt I had no control over. How does the MBR know which OS to boot from if they're on different drives? I have two SSD's. One which contains Windows 10, and right now the other one contains NO OS at the moment, but I'd like to run Ubuntu on it. Would I need another program to determine which OS I want to boot from on startup? If I install them on the same disk would that make things easier? How does this normally work?

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You're over thinking the issue. Grub resides in MBR of /dev/sda (the first hard drive). My laptop has an SSD (240GB) /dev/sda, a HDD (500GB) /dev/sdb and a mSata SSD (120GB) /dev/sdc. A Nautilus snapshot is provided for you to see:

enter image description here

When grub boot loader starts up you are given a menu to pick one of your various OS's to run and the right drive is automatically selected.

In the examples above two of the three drives have both Windows and Linux installed on separate partitions within the drives.

Oh yeah Windows 7 is broken on two of the drives...haha

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    Okay so I think what I'll do is just keep one SSD for both Windows and Ubuntu, even though I don't necessarily have to because grub is in the MBR and can allow me to select any OS from any drive? Aug 22, 2016 at 6:19
  • Correct @CarsonClark Aug 22, 2016 at 10:15
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In general, once you get GRUB to be the default boot manager you should be fine. However, windows has the annoying habit of resetting itself as the boot manager. I struggled with this for a long time. In the end, I managed to fix any issues I had by making windows set GRUB as the default boot manager.

If you encounter any issues like this, just type the following into an elevated windows command prompt:

bcdedit /set {bootmgr} path \EFI\ubuntu\grubx64.efi

NOTE: Type this command as is. {bootmgr} should not be replaced with anything, type the brackets as well.

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