In your root directory, just create an
/assets folder where you can put
/css', '/js', '/images folders like this structure:
|- application |- system |- assets |- bootstrap |- css |- images |- js |- fonts
And in your view template you can just call your assets like this:
<link rel="stylesheet" href="assets/bootstrap/css/bootstrap.min.css">
and you're done.
Btw, you just said that:
I also downloaded a bootstrap theme from startbootstrap and i moved css, fonts, images, js Into the root, where application folder resides
I advise that it would be much better if you put it on one folder, which in this case is
/assets folder, so it would be more organized.