I know the root word is ἐκκλησία, but I don't understand the declensions.
The different forms indicate different cases, somewhat like the difference between "he", "him", and "his" in English.
Ἐκκλησία is the nominative case, for the subject of the sentence, like "he".
Ἐκκλησίαν is the accusative case, for the direct object of the sentence, like "him".
Ἐκκλησίας is the genitive case, for the owner or possessor of something, like "his". (It can also be the accusative plural, like "them".)
There are a few others too, like the dative ἐκκλησίᾳ, if you're giving something to the congregation or doing something for the congregation, and an entirely separate set of plural forms, for talking about multiple congregations. The way of deriving all these forms is called the declension of the noun.
Ἐ is no longer used (the apostrophe in general) so it is just E Also Εκκλησία is used but Εκκλησίαν is no longer used, it is simplified to Εκκλησία at modern Greek. So accusative case is Εκκλησία as well. Now about (η)Εκκλησία and (της)Εκκλησίας is just as you say, nominative and genitive cases.