If I understand your question properly, all you need to do is place your three blocks inside a subsystem, and generate HDL code for that subsystem. You can generate code for any number of blocks at one time, with as much Simulink hierarchy as desired, as long as all the blocks used are supported by HDL Coder. To create a library of all block supported by HDL Coder, run the command hdllib at the MATLAB command prompt.
Once you have generated HDL code for your entire design you can use HDL Verifier to cosimulate with ModelSim inside Simulink, or you can generate a HDL testbench with HDL Coder and simulate the entire design/testbench combination in ModelSim.
The demos and documentation that ship with HDL Coder are designed to help with such basic questions of tool usage.
