Hello AshuraX-san!
I can understand why you have worries and concern in regards to secondary characters taking in more spotlight and screen time than the main characters themselves. Hm... It's somewhat difficult to describe how to make them more even, but I should use an example from one of my fictions, "Wandering Ship."
In order to make it equal (or almost equal... It's tough dealing with multiple characters and OTPs that you could count with possibly more than two hands together), I decided to break the story into two types of chapters/sections. There's one type of chapter where almost all of the characters are put into action. I try to keep in mind who is appropriate in the scene (as for example, Kimoto Kanon in my story is not the type of person to fight in battles, so to recklessly throw her into a huge group of thugs and emerge both victorious and unscathed is ridiculous. So easily Kanon will NOT be in any fight scene unless otherwise stated) and trying to make sure that each of them deserve equal screen time. I usually view my scenario like a mini movie flick or some sort of TV show in my head. Imagine each and every character as though they have a specific role that they must play out. Think about how the screen shows the scenario to the viewers. Same thing with fictions. I'm sure that the readers themselves and even you yourself will question multiple times to where in the world is Kuromochi Asuka after she dived into the water to save a fellow member of the crew within Takahashi Minami's viewpoint if her role isn't played/written out well. Last thing we want is to completely forget about her and focus only on Takamina, especially after the scene!
Now I'll also want to add that even if the character is done with their targeted goal/finish with their role, don't ever... EVER throw them out the window from your plot and pretend they never existed. Some fictions I've read forgot all about a certain character once the series had concluded. At least state the aftermath of what happened to them and reduce them down to minor roles so others can get a chance to shine. They're there in your story for a reason.
Second type of chapter is to focus on certain pairings/characters. It'll give me a chance to work on each and every pairing/character without having to worry who has the biggest major role and vice versa. Most of the casts in my stories will be given a chance in the spotlight as MC. Not to mention it's a great way to be able to develop relationship and bonds with the characters. Which is why there are pairing arcs with that story. No need to worry if your characters/pairings are overriding others!
I might be just ranting, but that's usually how I deal with fictions that have multiple pairings. But... I can't really say much since I personally think Wandering Ship is getting a little rocky with their new chapters.
And... my other stories mainly focus on either one or two pairings only, so yeah.
Overall though, try to at least shine the spotlight on other characters at least. Don't just always focus 24/7 on one character/pairing. Revisit the main character(s) constantly since they are given that main role for a good reason. As long as you keep that in mind, then you should have no trouble with keeping at least some stable equality among the cast.
Now for the secondary characters to have a much deeper impression on the readers than the main characters? That's completely fine. Not everyone is going to like the main character and who they are/what role they play.
Ah, I hope I helped you even if it's a little bit. Sorry if I wasn't able to help.