On the rack
Down at the end of the timber that has the machine clamped on you can see a short brownish batten standing fairly upright. That is screwed to the end of the timber with one edge along the pencil line that forms the vertical arm of the center line cross. I sight down to that aligning it with the depth gauge bar on the machine (perpendicular to the base plate) to ensure that the machine is oriented correctly on the timber. The flat area on the timber is very small, so it is possible to tilt the machine a little left or right using the pony clamps to align it.
One could use a spirit level on the base of the machine to perform the alignment, but there is a risk of the timber rolling out of alignment between cuts, so the batten is a better option here.
I have also made two marks on either end of the base plate that mark the point where the center line on the timber should be when the teeth of the chain are cutting the outside edge of the mortise. The chain is not wide enough to cut the width of the mortise in one go, hence the need for two lines, one for the left side and one for the right. I need to cut six times for each mortise and then chisel out a wall of timber left between the slots to complete the hole.
I have also made marks that indicate where the machine needs to be to cut the ends of the slots correctly.