I don't know any Manchester library for the DUE, however it should be rather easy to alter a Serialx (x = 1,2,3 or 4) to code/decode with the Manchester method thru a USARTn since, for what I have seen( in Manchester chapter, from page 782 of Sam3x datasheet), only US_MR and US_MAN registers are concerned.
The datasheet states:
When the Manchester encoder is in use, characters transmitted through the USART are encoded based on biphase Manchester II format.
Therefore the first question you have to answer is: does the equipment supposed to communicate with the DUE will be able to use the same Manchester Format ?