Upvote:1
Disclaimer, I don't know exactly how UA does this but...
The answer is 99% yes, provided the UA PNR (your itinerary), primary or linked, is associated with your MilagePlus account. This is how it shows up at united.com and in the app.
Also, there's long been the ability to specify different programs for benefits and accrual. But, different airlines have different support for this though I would expect UA to allow this.
You probably won't see the two options online for this. They really don't want you separating them. The only way to set this up ahead of time would be to call.
If the itinerary already shows in the app, you should be able to change only the accrual account at the Gate.