Hello and welcome to the Intel® Embedded Community.
The Intel® Atom™ processor E6x5C series packages an Altera Arria II GX FPGA on the same die as an Atom E6xxx processor. While there are many benefits to this integration, not the least of which are lower component count, board space, and cost, this product is a functional equivalent of separate Atom E6xxx processor and external FPGA components interfaced via PCIe. Combining the two components on the single die does not provide any "special hooks" from the FPGA into the CPU, it is still a PCIe interface. You might want to check out this blog below for a good introduction. Within the blog are links to more detailed technical specs.
I hope this helps.
J. Felix McNulty
Intel® Embedded Community