Let me firstly update you on my current situation:
HDD 1: solid state drive (GPT) with Windows 8.1 in EFI setup (no secure boot, has EFI partition)
HDD 2: regular hard disk (MBR) with Ubuntu 13.04 alongside a documents partition in NTFS.
Now it used to be like this ever since I reinstalled Windows in EFI. In legacy mode Ubuntu booted fine (when I override boot to my HDD 2 in BIOS), although according to the Ubuntu tutorials it's not exactly recommended to have two boot methods.
I want to install 13.10 as clean as possible, and I can now decide to change setup. What can you suggest I'd do? I know it worked fine in 'hybrid' (legacy + EFI) and EFI is the way to go, but I want everything to be coherent and streamlined.