Just in case "whatever the stencil is" is some horrible non-permeable coating reinforced with uber-slippery-plasticness that would prevent normal tile cement from getting a grip, I'd go with one of the two part (yea, a bit more expensive) tile cements.
But you could probably get away with just standard tile cement. Filling 1 mm isn't an issue - you can just ignore it. | 
Tiling over stencilled concrete nightmare 
aaaghhhhhhh (before puchase). I am about to lay a floating floor over the bulk of it. However at the entry points I am hoping to lay tiles. The floor is rough (not shiny and a nightmare to keep clean) and was probably very neglected in terms of sealing. The depth of the stencil is only about 1mm. Please can someone tell me what's possible. 
