Tom,
Usually, I model the foundation, including it's stem walls, on separate layers with the cripple walls above it modeled on their own respective layer.
The stem walls will be constructed with the slab tool with the appropriate gap to fit the door, and with the floor slab running through to pick up the door sill (just like you'd build it in real life).
The cripple wall will be placed on top of the stem, and will run right past the door gap.
The door will be placed in the cripple wall and it's header height adjusted to pull the door down into the gap in the stem walls.
That's it.
By modeling the stem wall with the slab tool I can handle three things simultaneously:
1. Have the stem wall show correctly on the floor plan with an empty fill (or stippled, or however you show finished concrete surfaces in plan view).
2. I can step the stem wall easily, and the end joints will 'heal' on sections and elevations, but show correctly in plan view.
3. I can have the stem walls show with the correct cut fill in a section, and control the plan view appearance as noted in 1.
And... If you have stems that are stepped on the top AND bottom, split the stem in two horizontally, use slabs for the top edges of the stems (so steps show in plan) and use the wall tool to make the lower portions (which will step with the footings and can be hidden by the slabs' cover fills above them in a plan view). This way, all the components will still 'heal' on an elevation or section view.
Do this all the time on sloped sites. The fun never ends!
Hope that helps.