Shell: There's really no right way or wrong way. Just whatever works for you.
In general, we take one room or section (branch) of the house and concentrate on that room or section (branch) during that week - decluttering and deep cleaning. Then, we maintain that room with our regular weekly cleaning routines while we move on to the next branch.
Sometimes we can't finish everything we want to do in that branch during the week. That's OK - we can get to those tasks when the branch comes around again, or, whenever we have time.

If a particular room requires longer than a week, then, we make that room our Room of the Month (the thread for that is over in the Motivation and Goals forum) and work on it for a month (some rooms take longer than a month and that's OK, too, while a few of us seem to have a Room of the Year - mine's the garage!).
*****************
The all-house branch comes at a good time for me (funny how each branch seems to come up at just the right time!) - it was so hot this past week that I didn't keep up with my weekly cleaning schedule. So, I've a bit of "catching" up to do:
- Living room: Dust/Vacuum
- Dining room: Dust/Vacuum
- Laundry room: Sweep, tidy up
- Bathrooms: Cleaned one yesterday; need to clean the other
- Kitchen: Cleaned it this morning! - wiped counters & stove top, cleaned microwave, swept and mopped the floor and shined the sink.
- Child's room: Vacuum; DD wanted to exchange one of her bookcases for one of mine - will see if she wants to do that this week.
- Guest room: Dust/vacuum; exchange the bookcase with DD's?
- Family room: Sweep, dust, clean sliding glass door
- Master bedroom: Dust/vacuum; tidy closet