SOPC + external Vhdl simulation

How do you plan to communicate between the SOPC and the other custom hardware in the 2nd FPGA?

I would try first to connect the custom hardware to the SOPC inside one FPGA for example over an AVALON MM interface. If that is verified (may be with reduced functionality) than you can implement the custom hardware in the other FPGA.

For simulation your custom hardware together with the SOPC you can expand the testbench which is generated during SOPC building. I case you are using VHDL the file <your_toplevel_name>_sopc.vhd contains a section:

-- <ALTERA_NOTE> CODE INSERTED BETWEEN HERE

--add your libraries here

-- AND HERE WILL BE PRESERVED </ALTERA_NOTE>

entity test_bench is

end entity test_bench;

...

Here you can instantiate your components. Additional you have to compile your sources in modelsim.

In Altera Version 7.2 I changed the setup_sim.do script in the <your_toplevel_name>_sopc_sim subdirectory.

Jens