For a vertical borehole, the Orient 3 value serves to define both Orient 1 and Orient 3.
For a vertical borehole, Orient 1, as defined in Dips, cannot technically be defined because there is no "top" of core, since the core is vertical. That is, there is no "top" line from which to measure an angle to the reference line. So you should simply enter 0 for Orient 1 since it is not actually used.
Orient 3 serves both purposes of defining the azimuth direction, and orienting the core within the borehole, by defining the orientation of the REFERENCE line on the core, with respect to north. Combined with the fact that the hole is vertical, that gives you all the information you need to correctly orient the core within the borehole.
For a vertical borehole, Orient 2 is either 0 or 180 degrees, according to whether the borehole was drilled downwards (Orient 2 = 180) or upwards (Orient 2 = 0).