<<Tom, what you are saying is that the second hydraulic system was trying to "fix" the first hydraulic system that failed.. but because the first system failed in a way that was unfixable (broken hose) then it just kept trying and trying and trying and thats why it got overheated? Was this the sound we kept hearing over and over?>>
Yes and it would keep on trying until you turned off the power transfer unit (PTU). This automatic feature is very nice in many circumstances eg engine failure. Because the main hydraulic pump on both yellow and green are engine driven, if you have an engine die, the PTU automatically kicks in to replace the lost engine driven pump... therefore you don't have to deal with an engine failure and combined hydraulic failure. The automatic function of the PTU is annoying when you have a fluid loss in one system.
<<If worst came to worst and both systems would have died... does the third system act completly independent to these two and would we have been fine with that third one? >>
Yes, the blue is indeed independent and the aircraft can happily fly with only one remaining hydraulic system.
That said you should be able to recover the overheated system after turning it off for a while and you would be back to two hydraulic systems as happened in your case.