To 'bypass' the List View Threshold, which also applies to libraries, you need to create indexed columns and use them to filter your documents in the views, but also you need to make sure that the returned items are less than the LVT.
That means, that if you index the column 'Created' and create a view that filters on Create <= [Today]-90, if this view returns 6000 items the view will not be displayed (assuming your LVT is 5000 items).
Moreover, if you create a view with multiple filters, make sure that the first filter is the indexed column. If you put as the first filter the non-indexed column the LVT will break it.
So for example, if your view filters on 'Modified <= [Today]-90' and 'Created <= [Today]-90', it will not work if the first column is not indexed, even if the second column is.