The stem direction option can only tell you if the note is flipped. This is
when the stem points in the opposite direction to the one which Sibelius
will use by default. 

Working out which way the stem points by default through pure logic is
pretty tough. The following basic rules can be applied but only for single
notes which aren't beamed.

If there is more than one voice used in the current bar, the stems on voice
1 and 3 notes will point up and those of voice 2 and 4 notes will point
down.

If there is only one voice , the stems of notes whose note heads are above
the middle line will point down and those of notes whose heads are below the
middle line will point up.

Notes whose heads are on the middle line will have stems pointing upwards if
the instrument is a voice and downwards in all other cases. This rule is
there to give lyrics more space.

If the instrument employs a tab staff or a percussion staff then the stems
will always point upwards, unless there is more than one voice, in which
case the rules governing multiple voice will again apply.

You must remember that the clef will change where notes appear on the staff.
In treble clefs C4 is on the first ledger line below and in bass clefs the
same pitch is on the first ledger above.