I have always either (A) booked the outbound flight online USING the companion voucher and then called back to add the return leg, or (B) booked the outbound online USING the companion voucher and booked the return online as a separate one way ticket using the full amount of Avios required and then called back the next day to get the companion voucher applied to the return leg and 50% of the Avios used for the return refunded. A results in a single booking for the round trip, B results in two separate bookings for each leg.

A should not incur fees when adding the return flight so long as the date of the return was outside of the schedule window when the outbound was booked. If you point that out they will waive the change fees (if they don’t automatically do so).

B will not incur additional fees either but does require that you have enough Avios to book the return using 100% of the Avios required (and get half refunded later when you call in). The advantages of B are that you can book the return online immediately the schedule opens without relying on a call center, and the fees are less because you are charged ex UK fees on the return and these are substantially lower than the ex USA fees charged for both legs of a return booking. Conversely, if you have to cancel then you are charged a cancellation fee for each of the one way legs, versus one cancellation fee for the return trip using A.

Either way, I would use the companion voucher on the outbound leg when you make the booking. They typically will not apply the voucher retrospectively except under the B scenario.