Well, mostly software can compute the % crystallinity of any polymer sample and if you know the enthalpy for a pure sample (what you get easily from the literature). Otherwise, you put in the formula and you can get the value. You can consult some good paper on the issue.
I don't see anything to complex in the thermograms, although the gas and initial temperature settings seem unusual (did you really start the scan at 0degC). The heating scan shows alot of moisture and the cooling scan shows a nice crystallisation peak. This paper will help you determine %crystallinity.
nothing strange in the two thermograms. PA66 is very sensitive to moisture that is released in the first heating scan where a clear melting peak is visible. Upon cooling the crystallization peak is also clear (from which the % crystallinity can be evaluated). Also, in second scan a clear indication of the glass transition temperature, Tg, of the amorphous part of PA66 (located around 70°C) is easily detectable, whereas in the first scan the Tg is masked by the simultaneous effect of the moisture content.
to correctly evaluate the crystallization peak you should calibrate your data taking into account that the initial sample weight is changed due to moisture evolution.