All configuration is done by writing data into registers and these are accessible by the processor. Within the datasheet of each module you find the registers affected and in the "Technical Reference" registers for building inrtra-connections are listed.
Technical reference manual (TRM) provides information about all the registers associated with analog, digital and other system resources. You can write into these registers during run time to configure any resource.
Here is the link for TRM: http://www.cypress.com/?rID=34621
For all parts in Designer you can go to "Help", "Documentation", "Technical Reference Manuals"
for the TRM manuals and datasheets.