I believe that they were good allies but were they also at some point became one nation. But it seemed like an unusually long "courtship" that lasted decades, or even centuries. That's why am kinda confused by the whole "Commonwealth" aspect. When and why did a "de facto" relationship become "de jure?" Could someone explain better on what that whole part of history was about.
The Polish-Lithuanian Commonwealth started as a "personal union" of the King of Lithuanian in 1386, when Jagiello married the Polish queen Jadwiga (who died in childbirth). That is, the same "king," ruled both countries, separately, not as a unified country. Under those circumstances, Poland and Lithuania became "fellow travelers."
Matters came to a head in 1569 for two reasons. First, the king of Lithuania threatened to die childless, ending the personal union. Second, Lithuania was threatened by Russia of Ivan the Terrible. So they sought a permanent union with Poland.
Poland wanted something in return, the de facto takeover of Lithuania. They didn't get quite this much, but the Lithuanians agreed to let the Polish gentry "settle" their holdings in the current western Ukraine, while preserving the core of Lithuania for themselves. This lead to the Union of Lublin in 1569 that formally merged the two nations, and created the Polish-Lithuanian Commonwealth.
After the Lithuanian (now Polish) king died in 1572 without heirs, the Commonwealth elected as its new king, a foreign prince, Stephen Batory, the first of many such foreign born kings.
Polish history twists and turns and is a bit "different" from the history of most other countries, which is why it's confusing.