Why is it important to repoint in layers? Wouldn't it be just as good to pack the mortar in one layer instead of having several layers that are not bonded together well?
Applying the mortar in layers gives you better joint compaction than applying it the full thickness at one time. It also ensures that the mortar joints are filled completely. If the subsequent layers are applied immediately after the mortar becomes thumbprint hard, and the surface is clean, there should not be a problem with bond between layers. The Brick Institute of America recommends applying repointing mortar in layers not to exceed 1/4 inch in Technical Notes on Brick Construction, Number 7F.