Retirement tax questions

Yes, I understand all of that. All pre-tax contributions must go to a 401K plan for example. How do you go about doing that and knowing how much growth is from those contributions and which growth goes with the after-tax contributions? Do you just rollover everything but the after-tax basis, assuming all the growth was on the pre-tax money to keep it simple? I'm waiting to hear back from etrade to see if they handle this.