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On this job, (below) which is typical, we started by removing a concrete slab which was installed when the house was built.
We actually had a small amount of clearance below the door sweep and could possibly have used thinset, but this would have raised the stone too high on the threshold. Secondly, since this is a North side, there would be icing issues in the winter, so we demo'd the slab and poured a new one.
The slab is just fibermesh concrete and we set it up to be approx. 1.5 to 2-inches below our finished surface. We also rake the finish on the slab to give the mortar a solid "tooth".
We used a pre-colored mortar mix with a latex additive to go with the stone, (in this case, Rainbow Flagging), and we use that as both the bedding mortar and the grout so we don't have to contend with grey mortar peeking through a grout joint. One color throughout completely eliminates that problem.
We start with the stones by the door since that's the most critical area. We make sure that the stone surface rests beneath the door saddle and we establish our pitch and levels from there. After we set a couple of stones, we grout them by simply slapping some mortar into the joints and tapping the mortar down with the edge of the trowel. Then we scrape off the excess and wipe everything down with a damp sponge. One wipe on each clean side of the sponge, then rinse and repeat. If you don't rinse the sponge between wipings, you're just smearing mortar around.
Then we just keep repeating the same steps until we're done. When we're finished, we'll give everything a light rinse with some muriatic acid and that's that.
If you have a large area to do and you can't finish in one day, make sure that you end on clean joints. That is to say that you don't have mortar oozing out into your work area for tomorrow bacause that will cause problems with setting the next stones and you'll likely end up having to chip it all out. Why make more work than you need?
I like to first scrape away the edges vertically and remove any excess mortar from the next day's work area. Then later, when the mortar has stiffened a bit, I scrape a bit more on an angle reaching under the work we just completed to create a hollow spot under the edge of the work we've finished.
Then, when we resume work, the next batch of mortar will be under-lap the previous work and acts as a type of scarf joint so that the joint is less likely to crack and separate all the way down to the slab.
The main thing with any cement job is to keep moving, keep a wet edge whenever possible, and clean up as you go.
Hope this helps!
-JP