When you specify the module (the VI in your case) for a step, you DO have the option to use a "relative" or an "absolute" path. The window that allows you to browse for your VI has a checkbox named "Use Absolute Path". If it is NOT checked then the path used will be RELATIVE to the TestStand Search Directories. If the module is NOT found in the TestStand Search Directories, you will get a window asking you whether to use an absolute path or to include the directory where the module is located to the TestStand Search Directories and thus, a relative path will be used.
When deploying your system, you can place the VI wherever you want. You will only need to include the directory where it is located in the TestStand Search Directories of the target computer.
You can find more about the TestStand Search Directories in the User Manual, page 4-34 (Chaper 4 -> Configure Menu -> Search Directories).
On another note, I am not sure what you mean by saying that you will build an executable. Are you talking about creating an executable out of the VI? If this is the case, be aware that the LabVIEW adapter is ONLY able to call VIs and NOT executables! In other words, you DON'T need to create an executable out of your VI when you will deploy your system. If you still want to create an executable and call it from your sequence, you will need to call it using the "Call Executable" step type.
I hope this information will be helpful.
Regards,
Carlos Leon