If using Jtag to program S6J3200 series MCU, please use User Mode shown below (S6J3200 series hardware manual: http://www.cypress.com/file/332246/download )
In addition, you can refer to the flashloader example included in IAR installation folder for programming via Jtag interface (eg. IAR Systems\Embedded Workbench 8.0\arm\src\flashloader\Cypress\FlashS6J3xx).
Detailed Jtag specifications required signed NDA to share. Please kindly contact Cypress Franchised Distributors (http://www.cypress.com/cypress-franchised-distributors ) or create a technical support case on Cypress website.