Actually...
UA and I'm sure others as well have the ability to enter multiple FF#s int to the system. I've done it actually. They specify 1 for accrual and 1 for status/redemption. May not be possible if you are booking online however.
I did this when I was flying SFO-LAS. I entered my NH Plat # for accrual and upgrade priority as a *Gold, and then specified my UA account as support for the upgrade (500 miler) if it cleared. (It did

)
Cheers,
Scho