What is the phase of tone?
If you want fine control over the phases, I assume you may also care
about having low phase noise. In this case your best bet is to avoid
toggling the pins in software and go for a hardware signal generation.

With an Arduino Uno or similar board, this can probably achieved by
programming a timer. I would try the following:

Configure Timer&nbsp;1 in waveform generation mode&nbsp;12, i.e. CTC
mode with TOP =&nbsp;ICR1. Set the compare output mode of both channels
to toggle on compare match. Set ICR1 so that the timer has half the
period of the signal you want. Now you can independently adjust the
phases of both outputs by writing to OCR1A and OCR1B.

Note that those registers are not double buffered in this mode, so you
have to be careful about when you write them.

The Arduino core library has no support for such timer configuration:
you will have to learn how to program it yourself. If you are not
familiar with the subject matter, I recommend you start by reading
Nick Gammon's tutorial on timers.