How to use <ALTERA_NOTE> section for NIOS II simulation

Hello,

Now I am trying Nios II simulation using ModelSim.

ModelSim is started by Run of Eclipse.

Before adding code to <ALTERA_NOTE> section, it works well.

I want to add some RTL code (including additional logic module).

additional modules are stored in different directory from Simulation directory.

I used menu of File > Source Directory to add location of new module .v files.

But I am facing following error.

** Error: (vsim-3033) ../xxx.v(14053): Instantiation of 'yyy' failed. The design unit was not found.

Does somebody know how to add additional module to ModelSim.

My environments are

Quartus II 11.0 Web Edition (32-Bit)

Nios II 11.0 Software Build Tools for Eclipse

ModelSim-Altera 6.6d (Quartus II 11.0) Starter Edition

Thank you.