Maternal and paternal designations are made by FTDNA based on the
identification of matches on your family tree. If one match sits on your
mom's side, FTDNA says its maternal and anyone else who matches this
person will be assigned on your maternal side.
After you have assigned test results to relatives on your family tree,
FTDNA will know who is a maternal or paternal match (provided the
matching is above a 9cM threshold on any individual segment). Someone
who matches one individual already assigned as, say, maternal to you,
will also be a maternal relative and so on.
Hope this helps,
Rio de Janeiro, Brazil