Dear Joe,
Embedded Wizard Studio is used to create a user interface application in a platform independent way. The idea of Platform Packages makes it possible to run every UI application on a certain target hardware.
The interaction with your hardware components (e.g. the communication via SPI, CAN, I2C, UART,..., and GPIOs) is part of the underlying software stack (drivers, middleware, BSP, ...) which is not part of Embedded Wizard.
All the necessary aspects to interact with your hardware are described in the article Device Class and Device Driver.
However, all the details concerning your dedicated hardware (e.g. GPIOs, SPI, CAN, ...) can be found within the documentation of your microcontroller / development board / board support package.