Is the "i" ending always for masculine and is the "ae" ending always for feminine?
Almost all second-declension nouns in -us are masculine and most first-declension nouns in -a are feminine, but there are exceptions.
For example, nauta (sailor) and agricola (farmer) are both masculine and have the plural nautae, agricolae. methodus (method) is feminine and has the plural methodi.
(Most feminine second-declension nouns seem to be loanwords from Greek, like methodus from μέθοδος.)
It's not appropriate to use the accusative case here.
There is no verb taking a direct object. (Hint: you can't make a passive sentence out of this, "students are being been by many boys".)
You need the nominative case for both the subject and the predicate of the verb "to be".