These can be quirky but I can get you started.

You'll need both 8889-T and 8889-S.  You'll mark on both forms on the Line 3 Smart Wks that they have Family coverage.  There's a line 6 Smart Wks where you can allocate the $6,900 amount between the two of them (mostly ProSeries takes care of this automatically though).

The "extra" $1,000 each doesn't kick in until line 7 of each separate 8889 so it isn't (and can't be) allocated between spouses.  Sounds like you know this though and kinda know what you're doing, you're just fighting with the data entry.

You mentioned encountering problems by marking them both as covered under a family plan, what problems are you encountering when you do that?

Rick