"First, where to do the classification and marking? swicthes or remote router?"
Ideally as close to the source as possibly, including on the source host itself. For the latter, though, you often should do verification as close to the source too. Again, that's the ideal. Often, when dealing with constrained bandwidth links (often WANs) I've done all that was really needed on the bandwidth constrained interface within an egress QoS policy.
"Second, In remote site the connexion between router and switch is trunk, How can i configure the Qos between the router and the swicth?"
On switch, QoS is effected on trunk interface and L3 switch, possibly and on SVI(s). On router, QoS is effected on subinterfaces and/or main interfaces.
Possibly as important, if not more so, what do you want your QoS to accomplish?
BTW, QoS features and defaults vary between platforms, especially switches. Also switches usually have more limited QoS features compared to routers.
Lastly, if QoS is new to you, "book" QoS recommendations are usually more complex than actually needed, and often are not nearly as effective as they can be. BTW, I suspect "book" QoS's complexity and overall ineffectiveness is why QoS is overlooked.
