There are no middle names in Portuguese culture, so that field should be empty in Portuguese profiles. We should not put there family or given names just because it would look better when it is displayed in some pages.
If the family name of a person has more than one word they all should be put all together in the relevant surname field (LNAB, Current Last Name, Other Last Names).
Before XX century there were no law or rigid rules about the transmission of family names(1), and was common siblings with same parents to use different surnames.
If the only source is a baptism record with just the given name and parents names you can not be sure what was the surname if the person. In this case I put in the research notes of the profile the disclaimer: "It's possible the surname is not correct (source does not have a surname). At this time and place it's common siblings with same parents to use different surnames. Following current WikiTree standard (Dec21) surname of the father was arbitrarily used in order to avoid another unknown surname."
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(1) Monteiro, Nuno Gonçalo. “Os nomes de família em Portugal: uma breve perspectiva histórica.” Etnográfica, vol. 12, no. 1, May 2008, pp. 45–58. SciELO, http://scielo.pt/scielo.php?script=sci_abstract&pid=S0873-65612008000100003&lng=pt&nrm=iso&tlng=pt.
"Family names in Portugal: a brief historical overview
This essay constitutes a first attempt to study a theme which, in spite of its enormous importance, has received little historical attention: the evolution of the Portuguese practices of anthroponymy that had a worldwide impact due to Portuguese imperial expansion. The author contrasts the changes that occurred at the turn of the twentieth century to the practices that were prevalent among the Portuguese aristocracy ever since the great changes that took place at the end of the Middle Ages. "