Hello , Please i have a questions concerning phylogenetic analysis using Mega

Please i have some Phylogentics analysis using Mega i have set of data (mitochondrial DNA of mammals) of different superorders and orders , my objective is to detect monophyly in specefic superorder , for that , i m working with 26 species of my superorder and one species from each other superorders and orders i have in my data i'm using Neighbor joining but i don't what values of paramters i should use to get better results ( type DNA or proteins and which model , and if i should use all the species from the order i want to analyze and just one species from each one of the oder orders supeorders )

Please tell me if you have any thoughs or suggestions about this Thank you very much