Regarding the cover.tex
file,I have a suggestion. I couldn't change the department information of my supervisor, but then I solved the problem after 10 or 15 minutes.
I noticed that the supervisor's department was by by default "Departamento de Eletr贸nica e Comunica莽玫es", as I quote here, from the page 4 of the cover.pdf
:
Disserta莽茫o apresentada 脿 Universidade de Aveiro para cumprimento dos requisi-
tos necess谩rios 脿 obten莽茫o do grau de Mestre em Engenharia de Computadores e
Telem谩tica, realizada sob a orienta莽茫o cient铆fica do Doutor Tiago C. A. Oliveira,
Professor auxiliar do Departamento de Eletr贸nica, Telecomunica莽玫es e Inform谩-
tica da Universidade de Aveiro, e do (...)
And when I changed the supervisor line of cover.tex
to this:
\Supervisor{Tiago C. A. Oliveira}{auxiliar}{do Departamento de F铆sica}{da Universidade de Aveiro}
I got an error when I compiled the cover file. Then I solved the problem because I realised that I had to change the department information to fis
on the line \usepackage[engineering,fis]{uaThesisTemplate}
So, my suggestion is for you to put a comment on that line on the fact that we have to select the department first (the emphasis of the department information is at the moment less relevant, at first sight, due to the fact that the department is, by the new rule of Univ. of Aveiro, not printed in the first page of the cover.