Make sure your gerber files are in order. The program uses a "1 pcb = 1 folder" rule. Do not put files from different boards in the same folder - this will end in tears.
.txt or .xln = excellon drill file.
.gko = outline file.
.gml = mill file. MAKE SURE YOU DO NOT INCLUDE THE BOARD OUTLINE IN THE MILL FILE AGAIN!!!
gbl/gbo/gbs/gtl/gto/gts and the above will be used for image generation
all other files (if gerber) will be combined with files with matching extension (case insensitive!)
Start a new document or load an older one (this can also be done by dragging folders to the main area - this will start a new document and add all the folders)
Add folders that contain the files for -1- PCB at a time. (or drag a folder to the board - this will add an instance)
Drag instances around until you are happy. PLEASE MAKE SURE TO KEEP AT LEAST 2 MM BETWEEN THE BOARDS - the mill the boardhouse uses to separate the boards is not infinitely thin!
Add tabs breaktabs by rightclicking and adding tabs. A good guideline for tabs is to keep them about 3 or 4 mm wide, and have one about once every 3 cm on a shared side. Try using 2 tabs as a minimum for each connected board or you might get a handful of separated boards back from the post because they broke off (this happened to one of my tryouts)
Edit instances in the treeview or numerically
Make sure you dont have crosses or floating stuff that might end up loose.
Export the combined thing and enjoy your new gerbers/images.
Issues/bugs/known things:
geometry is not always perfect.. always use sanity and check the exported gerbers like you would usually do before sending anything to a factory.
interface does not always directly update after a number-edit. drag something to make it recalculate the output.
yes the userinterface could do with zooming/moving/3d/partrendering/autorouting and all that stuff... my time is not infinite.
merge is currently slow but acceptable. boardimages are slower. (but the merged files should be done before the images anyway.)
paths saved in the set-files are absolute.
boardhouses might reject your generated boards. I have exclusively tested this tool in combination with the services provided by DirtyPCBs.