What I want to do, is to set the Fn key as a toggle (same as caps lock).
I was thinking this should be possible through registry, but I do not have enough knowledge of it to fix this. (Could also be inverted, so that when I hold it down I can use the F1 - F12 keys).
It's quite possibly not possible, I'm afraid. Usually the Fn key isn't something that's passed to the operating system, but rather implemented in the keyboard's firmware.
Take my laptop, for example. Fn+F3 is mute. If I (on Debian, but the same principles apply to Windows) run showkey --scancodes, to see what my keyboard is doing, I get no output if I press and release Fn. If I press and release F3, I get ^[OR0x3d 0xbd, and if I do Fn+F3 I get the entirely distinct scancode sequence 0xe0 0x20 0xe0 0xa0. Compare this to the situation with ctl: press-and-release gets:
0x9c
0x1d
0x9d
And ctl+f3 gets:
0x1d
^[[1;5R0x3d
0xbd 0x9d
As you can see, Fn isn't passed to the OS; it directly changes what the OS can see.
So short of changing the keyboard's firmware chip, and unless it already has a Fn-lock key as Michael Frank commented, turning Fn into a toggle is not going to be possible.
The inversion option, however, is doable. There may be an option for it in the BIOS, but if not, you'll need to find out what windows thinks the scancodes of both the F1-F12 keys and the result of Fn+[those] are. For each key, you'd swap the result of its fn+key scancode with its unmodified one. This is something that can be done on Windows with regedit, though there are probably easier tools, and on Linux with the appropriate tools, probably a text editor and setxkbmap. Unfortunately, I can't help you with that.