You can board with her in Group 2 - it doesn't matter what boarding group number is on your boarding pass - just have her tell the gate agent "She's with me" as she has her boarding pass scanned. Your boarding pass will not indicate your companion status, whether or not the reservation is split. As for the upgrade thing - prior to check in (and if one confirmation code contains both travelers' names), you are both eligible for an upgrade at her status. At check in, there's an option to split the reservation, in which case she shows on the list and you don't (because at that point, UA's IT no longer recognizes you as a companion). You can be added to airport list (the one you can see) at the airport, but that's usually futile by then. You can still get her bag allowance if you want one after a split of reservation - the check-in counter agent can see the records were originally one - just be sure to waive down an agent before using a kiosk.

Edit: Corrections below