Did the German SS flags have the skull and crossbones on them

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Not on their flags, no. They wore a death's head skull as a collar insignia.  

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The 'skull and crossbones' is infact the insignia of the SS 'Totenkopf' or Death's Head division. This was one of the first divisions of the Waffen-SS to be established from the SS-VT. The Totenkopf division was responsible for, amongst other things, the running of the concentration camps  

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The Skull & Cross bones, called Totenkopf (Death Head) in German, is an old symbol dating back to the time of the German Empire under the Kaisers. The symbol was a badge of honor given to troops that particpated in the funeral ceremony of emperors. Later, during the Hitler period, the symbol was used by units considered "elite", i.e. the S.S.
There are some British tank units that had a similar collar device, but I do not know the history of how they came to be.  

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The armored forces (panzer units) also used the "totenkopf" collar device and were sometimes mistaken for S.S. troops when captured. SS units wore an eagle insigna on their left upper sleeve, while wehrmacht troops wore it on the breast.  

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The SS Divsion "Totenkopf" did have the skull & cross bones on their divisional flag.  

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The skull and crossbones go back to some Prussian guards cavalry units and became part of their official insignia in 1740 under Frederick the Great. One Prussian Hussar (light cavalry) regiment was dressed in black and had a tall hat with a complete skeleton insignia on it. I believe their motto was "Death before Dishonor"--same as the SS. Later in WW1, this Hussar unit wore a fur busby with a chapless skull & cross-bones.
The British 17th Lancer Regiment used the skull and cross-bones as their insignia and cap badge. This unit dates back to the "Charge of the Light Brigade" during the Crimean War. During WW2 this unit was an armored regiment. There have been many other units in other countries that adopted a skull as their insignia. During WW2, Italians had a unit called the Black Brigades or Brigate Nerre, that used an insignia of a skull with a dagger clenched in its teeth. There are many examples of skulls used in US Air Force and US Navy squadron patches during WW2 up to present day.
The German Panzer units wore a small chapless skull sitting on cross-bones mounted on a black collar tab with pink pipping. The SS Divsion "Totenkopf" wore the Skull on one collar lapel and the SS-runes on the other. But this was unique to this division as was the flag mentioned, above. The regular SS wore the skull(with a jaw) on their caps, under the eagle branch insignia.
Custermen  

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I'd like to point out, since nobody seems to have done this yet, that the SS flag was black with two sig runes ('lightning bolts') in white spelling SS.





You can see an image of these flags at : see related link