There is basically no difference from a communication perspective.
- If the Arduino is the master, it will send data to the FPGA or request data from the FPGA. You will need to know what kind of 'commands' the basys3 supports.
- If the Arduino is the slave, study what the basis3 requests and what kind of replies it expects.
Your topic has been moved to a more suitable location on the forum. Installation and Troubleshooting is not for problems with (nor for advise on) your project
See About the IDE 1.x category.