A little late.
To two hole a flange means to have the two top holes of a flange straddle the vertical centerline of the flange. This is easily accomplished using two pins that fit the bolt hole and make the pins level while still straddling the vertical center line. This can be accomplish by experienced people with just a level lined up with the top or bottom of bolt holes. This method is very accurate.
If a single bolt hole straddles the vertical center line is said to one holed. This method is hard to do in the field.
Using the two hole is mainly for allowing individual piping spools to line up when assembled. There are other reasons, like inserting a gasket by removing fewer bolts.