How to Output DDR data to 1 register
The normal procedure is to use double the data width inside a DDR receiver. 

So with a 12-bit DDR bus you must output the data to a 24 bit wide port/register. 

The alternative is to use double the clock frequency (or higher) inside but as you said that is often not an option. 

You would NOT keep processing the data internally on alternate clock edges. That is bad design.