Pin Assignment for Custom Component in SOPC

I am working on DE3 board with Stratic III device on it. I have successfully written a piece of verilog code which deserializes the LVDS data coming from HSTC port (an external ADC ic connected to HSTC). Earlier, i was able to develop a NIOS based system which can read data from memory on FPGA and send it to PC via USB link.

What i am tring to do now is to send the deserialized data in verilog module to PC using NIOS. For this, I made a custom block which includes all verilog of the files and SDC file of my proj ( unfortunately i cannot include pin assignmets, pin planner settings, logic lock region assignments...). The problem is that my code has no inputs as it is reading data from FPGA pins. So just the pin assignments to proper wires was working for me (as inputs) and the output i had was deserialized data and clock in the verilog project. These outputs are treated as streaming output in SOPC.

Now in the custom component, i can not assign pins to the wires as this module of mine is not a TOP level module ( and i dont know if it can be as it is a component of the whole system). I tried to have an input of this module and send this input using top level module where i do the pin assignments. I can do this in Verilog files genrated by SOPC builder. But i do not know how do i make this (input) connection for my custom block in SOPC? what interface it should be? ADC is workin at 50 MSamples per second, so i do not want the HSTC inputs to be going through NIOS as deserializing is very time critical issue. I am totally lost over here. Any help will be appriciated.