(See the best response by Kaiochao.)

Problem description:
So I have a main window but i also have windows in my interface that are things like pop-ups, and input alerts and would i make thoe etra windows "stay on top" at all times.

(Basically if i click on the map, the extra windows won't diappear behind the main window)
I'm not sure, but setting the focus parameter of the window to true on a loop might do it. I'm pretty sure there's a request out in the wild for an 'always on top' setting too, but I'm not finding it off hand.
so..... winset(src, "Alert Window", "focus = true")

would that do?
I actaully don't see any focus parameter in the BYOND Interface Control Guide
It's listed under 'all'.
Oh, I saw it already and I was correct. Hopefully it works. I will let you know
It didn't work
Show what you tried exactly, I can't test myself right this moment but I'll have a bit of time later to see if I can find something that works.
winset(M,"Alert","focus = true")
And the window is called 'Alert'? Have you tried focusing an element within the window? And remove that space around the equals sign, that's just horrible looking.
Yes sir, its called Alert. Hm I haven't tried that, but i will soon. A little busy at the moment but i will let you know. But it would still be great to see your work-around and lol, your way looks horrid to me o.o
You could also try loop-calling winshow() on the window.
But that wouldn't be efficient though, right?
Best response
It would be more efficient to do it in JavaScript, which runs client-side, but... popup windows never go behind the default window in the first place.

It's weird that your popup windows are disappearing behind your main window. Is your main window not actually the default window?
I realized, at my login i set the login as the default window....then after logging in, I used the
winset(src, "MainWindow","is-default=true")

But for some reason it doesn't actually become the Main Default Window. Instead on my Task Bar (for example) it shows up as Options and Messages.
Changing your default window at runtime usually isn't ideal. You should make your default window something that contains a child control so you can shift what's inside of it easily.
The issue with that is, my Login screen is a username and password type of login and its design is way smaller than my MainWindow's size. Is there any other way?
You can change the size of things if needed, but ideally it should be designed yo handle that. Having a single default window is going to save you a lot of headaches like this.
Yeah, i already figured it out. I just adjusted the size of the window to fit the Login pane.