So my first question is "Did you treat your villain as the most important character for your story?" If your answer is no, stop right there, and beep beep back the truck up.
Your villain is going to be agency of the entire plot. There's no story about your heroes without the villain so you need to know the villain as well as we know your hero, if not better. It's a lot of work... but the good news is, you the storyteller only have to do four things with the villain to make him better. Simply answer the following four questions your audience will ask the villain: "Who are you?" "What do you want?" "Where are you going?" "Why are you here?"
We can look at any good villain and see the answers and some maybe more important than others. Consider the last scene with Thanos in Avengers: Infinity War. By the end of the film, we know the answer to all of the questions posed to Thanos.
Who is he? Thanos, the Mad Titan and the sole survivor of race too foolish to heed his advice, an intergalactic warlord who seeks not conquest or glory, but order in all things, the adoptive and deeply loving father of six children who cares for them despite their disagreements.
What does he want? The six infinity stones so that he may kill half of all life in the universe, so that the other half may survive an inevitable environmental cataclysm brought by overpopulation and limited resources.
Where is he going? No where, as he has succeeded... though the film is about him getting to the "snap" successfully.
Why is he here? To recover because the Snap was taxing and Thor did not aim for the head. Because he has won, but there was a price.
The first two questions are best using a literal interpretation. The first asks, prior to the the story, who was this person... what happened to him, and what was his life like and the second is purely about the win condition for the villain. To answer the first, you need to show the steps prior to the villains conflict with the hero... and since no one is evil, what caused the start of darkness. The second needs to show the thought process between the answer to the first, and the ultimate goal. Thanos was told that killing half a population to save another was crazy... yet all but he died... and because he doesn't want to see another civilization die because of the mistakes of his, he will make the choice for everyone.
The third and fourth are more metaphoric and speak to the progression of the story and are constantly updating. Where are you going speaks to the steps between the beginning and the end of the story and will probably be the hardest to answer. In the case of Thanos, his answer over the film changes from "Thor's Ship" to "Knowhere", to "Thanos's Ship" To "Volmire" to "The remains of Titan" to "Wakanda, Earth" to "The Garden" over the film's run. The final question is immediate now related and asks why is the villain in this place right now. Given the answers to all the stories, this can be the easiest to answer... With exception to "the Garden" Thanos is "here" because there is an Infinity Stone here as well, and he needs that for the answer to "What do you Want?"
With that in mind, you should be able to say here's the villain, here is his goal, here is the steps of the story where our heroes will face him, and here is the reason for each of those steps.
Your biggest bad guy will only lose once (at the end of the story) and if he directly confronts the hero(es) before the final battle, the villain must be a clear threat to all. Except for the climax, when the two meet, the hero is on the defensive and "wins" if he survives the encounter with the villain's ability to persue him momentarily disrupted. The villain doesn't win, so much as temporary stop a threat to achieving a goal. I always recomend that the villains be encountered sparingly. There are very few times Darth Vader and Luke Skywalker are in the same room together and Luke is the best chance the rebels have in a fight with Vader... and is not as good as Vader in combat. In the original trilogy, they are barely in the same room in IV, once in V, and twice in VI (if you count the scene on Endor as seperate from the Death Star). Vader's menace is that he's difficult to beat for Luke and impossible to beat for anyone else... but he's rarely encountered by any heroes... but the first time you hear his signature breath in any scene, you know the good guys are in big trouble.
If you must have frequent fights, minions are good places, but the villain may send the minion to accomplish a goal that doesn't matter to the villain if the heroes succeed. The character David Xanatos in Disney's Gargoyles was famous for this kind of plotting. It was quickly noted by fans that Xanatos' goals were not counter to the gargoyles goals. For example, one episode a robot duplicate of his frees five members of another foe of the Gargoyles, the mercenary group "the pack" from prison (only one of the five is left in jail).
It doesn't matter to the real Xanatos if the Gargoyles don't stop the Pack's crime spree, as his goals are achieved, and if the Gargoyles do stop them, he can get more data from the robot duplicate. In fact, the crime spree itself doesn't matter to his plan. The real reason he broke out the Pack was so the one left in jail could do so by refusing to break out... which impresses the paroll board who grant the remaining prisoner her request of early release... and we then learn that Xanatos is dating her so his goal was won before the Gargoyles could even make a choice to act or remain out of action... If the pack is allowed to run free, that's fine, as it still shows his love has reformed. If they are stopped, then dangerous criminals are recaptured and his love still appears to be the lone reformer... getting more data from the Bot was just the icing... the Xanatos had the Cake in the opening five minutes of the 22 minute story.