If you are asking which voltage to use (for example, 120 or 208), when you figure out the percent VD, the answer is that you use the phase-to-phase voltage (in my example, 208).
You can do either, as long as you pay attention to which you do. I prefer to calculate L-N drop since in a balanced 3 phase system there is no neutral current.
The equation that I use is current X distance X z(from Table 9.)/1000.
That is your basic equation E=IR.
To calculate %drop, I divide the above # by 120 for a 120/208 system or 277 for a 277/480 system.