Is it a issue to achive proper QoS for IP tunneled traffic over GRE encrypted by IPsec tunnel – for Cisco router is not the case. With use of GRE/IPsec ToS byte is copied from the original IP header to the new GRE and IPsec IP headers. It’s done by default without any specific configuration, this process is called the „ToS Byte Preservation” feature.
For example if router gets IP packet with DSCP value equal to 46 then packet is encapsulated in to GRE header, ToS byte is copied to the GRE IP header ToS field. In case this GRE packet is subject to IPsec encryption the same process occurs and ToS byte from GRE headers is copied into IPsec IP header – all is done by automatically. But what if QoS policy would classify and do action based on original source IP and specific TCP or UDP port. Solution is the QoS pre-classify feature. It allows router to temporarily copy and store the layer 3 and 4 headers from the original IP packet and take action based on these values so classify, queue and schedule on the router’s egress interface accordingly.

To achive above QoS feature have to be enabled both under GRE tunnel and IPsec crypto map as follows:
Router(config)#int tun 0
Router(config-if)#qos pre-classify
Router(config-if)#exit
Router(config)#crypto map MAPA 100 ipsec-isakmp
Router(config-crypto-map)#qos pre-classify

Now you are ready to go with class-map and policy-map. Remember that in this case policy needs to be assigned to physical interface where crypto map is configured already.