It sounds to me that you first need a plan including architectural design, structural design, energy compliance etc.
Once those decisions are made, then you will know where your bearing walls and shear walls are. This will determine all your footings and hold downs.
All hold downs and anchor bolts in California, must be in place for the pour. It does make finishing more difficult.
As said above you can drill and epoxy threaded rod after with a special inspection. You could also check out Simpson titan bolts for wood plates.
I am curious, why you are using CMU's? How do you plan on achieving your insulation values?