Ok then--
make black layer, and include the crop marks as black vinyl-- weed and then apply whole thing to white vinyl. - Place in machine then cut the next layer, which would read the crop marks and then cut the squares.
verify that your software has this capability-- reading crop marks, and transferring a "bank" of decals to the white will be the hardest parts--i.e.
The other solution may be to have them printed ( thermal / eco-solvent) if they are for outdoor. try and install the finished product yourself also - see if end result would be acceptable to your customers.