We had issued four invoices for 1M yen to the customer, two of which were already settled.
We had issued four invoices for 1M yen, two of which the customer already settled.
The customer already settled two invoices out of four issued.
１つめと２つめは、質問文を割と丁寧に訳しましたが、過去完了や"which"の使い方を誤りやすいと思います。とくに、「～のうち」や「～の両方」という際に"which"を使うと、","を使い非制限用法にする必要がでてきます。
ex1) She has two sons, both of whom are doctors.
ex2) There are two apples on the table, both of which went bad.
個人的には３つめの文章がすっきりしていて良いと思います。
日本 
