Prepare layout:
Before printing, make sure that *no* layer has features reaching beyond the markers
Otherwise, the markers will shift slightly when mirroring the layout during printing
The tNames/bNames or tValue/bValue text is a likely candidate for this
Fix: Smash the offending parts, delete the text
Tape a piece of paper to the bottom of the tray, print the top layer to it
Cut the PCB into size
Saves etching solution and time
It might be a good idea to file away the burrs (DE: Grat), they'll wreck cloth and paper during cleaning and priming
Clean and prime the PCB, put it into the tray so that it covers the print on paper, print the top layer, cure ink as usual
Drill two 1.5-2mm holes through the exact center of two of the markers
Copper is hard to drill, don't use your precious PCB drills for this
Try to make this drill as precise as possible, your layer alignment will depend on it
What worked for me: Prime the drill with a _precise_ punch mark (I used a large screw and a hammer), position the drill without power, then start drilling
Remove the copper burr (DE: Grat) on the other side!
Don't forget this, or the print head will scratch across the burr and smear ink!
I used a larger drill that I simply turned by hand
Clean & prime the still-empty PCB side
Put the PCB on the tray and align it so that the marker dots are in the exact center of the holes you drilled
Hence the circular shapes – the human eye can see deviations from a circular shape pretty well
If your holes came out slightly misplaced, use the two most precise holes for this and take into account their misalignment
Fix the PCB in place
The primer will prevent some tapes from sticking properly, maybe double sided tape to the rescue
Or just tape the PCB in place before priming and prime later
Print the bottom layer (mirrored!) and cross your fingers
If alignment is „good enough“, cure ink and etch