The entry point for reading and writing Cifti data is the object CiftiFile.  To get a handle to a Cifti File, use the following syntax:
CiftiFile *cf = new CiftiFile("testciftifile.dtseries.nii");

The Cifti 1.0 API breaks the file up into three logical sections, the Nifti 2 Header, the Cifti XML meta data, and the Cifti Matrix data.  To access the data use the following functions:

//read/write nifti header
Nifti2Header header;
cf->setHeader(*header);
cf->getHeader(*header);

//read/write Cifti 1.0 XML extension "header"
CiftiXML xml;
cf->setCiftiXML(xml);
cf->getCiftiXML(xml);

//read/write Cifti matrix
CiftiMatrix *matrix = new CiftiMatrix();
cf->setCiftiMatrix(*matrix);
matrix = cf->getCiftiMatrix();

//writing to a new Cifti File
cf->writeFile("outputfile.dtseries.nii");

For more detailed information on how to manipulated Cifti data, look at the doxygen documentation, located in the doc sub-directory, and the Cifti 1.0 specification, located at the following URL:
http://www.nitrc.org/plugins/mwiki/index.php/cifti:ConnectivityMatrixFileFormats
