Don't confuse split PNRs with the "split/no-split" indicator with respect to upgrades.

If your companion is linked to your account, using your status, they will be one notch behind you wrt upgrades, even if you clear and they don't. If they aren't the next one upgraded, it's because someone with higher status than you joined the list.

As to whose account they come out of, they have been coming out of my account (i.e., the higher status one).

Whether that is the only way to do it, I don't know.