Just cut up so you can fit your pipe there, but make it a little larger so you can fit the mortar, don't be too stingy with the hole, about 1 cm around the pipe is just right. If it's too narrow between the pipe and the stone, it won't get filled and can become leaky. You may need to spray some water with a spray bottle on the brick; too dry is not good. Then start poking and filling from the bottom around the pipe and upwards, as deep as the stone is. As for leveling, how do you mean? The pipe will end right where the channel begins, so there's nothing to level out. Smoke is like water, it takes the easiest path, and you should have a clear drop down for the soot and take it out from there.
Thank you @Liteavvarje.
The thing about leveling, I was just thinking if the bruk between the bricks looks like this:
Apply bruk on the inside so that it becomes smooth and nice. But it probably doesn't matter.
It's up to you if you manage to get the bruk there, (self-esteem) water the stone a little, apply bruk, level it off and fetch about half from the basement, maybe not with a cardboard piece in the hole so it doesn't fall down.
