As per the documentation https://github.com/matrix-io/matrix-creator-quickstart/wiki/Hardware
They have given a platform to program a bit stream to the FPGA, but can anyone guide me on how to go about designing custom logic ? and how to integrate ?
There are some good tutorials here on Element14 on VHDL programming. These could help you better understand the language and processes associate with designing custom logic for FPGAs.
I have written some tutorials (based on different tool sets), linked in the following blog post.