Question: If USB 3 is backwards compatible, why do they place USB 2 ports with USB 3 ports on motherboards?

Also, do USB3 External drives not work with USB2 ports?

Answer: 
USB 3.0 is fully cross compatible. 

USB 3.0 devices will run at 2.0 speed when hooked into a USB 2.0 port. 

USB 2.0 devices will run at 2.0 speed when hooked into a USB 3.0 port.

The USB A connectors for 3.0 have a second set of contacts that will not touch anything when plugged into a mating 2.0 termination. USB A connectors are typically used on the computer chassis. Any A plug will plug into any other A socket.

The USB 2.0 cable is the universal cable that should work with anything. USB 2.0 cables will plug into USB 3.0 peripherals, but USB 3.0 cables can't be used with USB 2.0 peripherals.

The B and mini USB 3.0 plug ends are structured such that they will not plug into USB 2.0 sockets, conversely, the B and mini USB 2.0 plug ends are a subset of the 3.0 connector and so will easily plug into a USB 3.0 peripheral socket.

USB 2.0 is older technology, there are still a lot of devices out there (who needs 3.0 for a keyboard or mouse?) and the 2.0 support chipsets are cheaper so you will see a mix for some time yet.

Most USB 3.0 based external drives will probably need a special driver (especially Western Digital) installed before the drive is fully usable on either connection setup. They work on both speeds of port, you just have much slower access on a USB 2.0 port.
They place USB 2.0 ports on a motherboard with USB 3.0 ports because USB 2.0 ports are cheaper, not everything requires a USB 3.0 connection's speed, and everyone hates to run out of USB ports.