Retirement tax questions

Schwab's experts keep telling me that with the 8606 form I will not have to pay the penalty and be taxed additionally in this instance. That the whole point of the 8606 is to not have to pay taxes even in this situation. Wouldn't line 6 on the 8606 form where I specify my balance in the Traditional IRA handle this issue? Or does the pro-rata rule still apply regardless?