Only these two properties control the z-order of windows: Form.Owner Property (System.Windows.Forms) Form.TopMost Property (System.Windows.Forms)
It sounds to me you want 'owner' more than 'topmost'. You could even dynamically assign some tool windows owner to the current active form on its Activated event.
In addition modal dialogs are also displayed on top of active window (or owner), and will block access to other windows in app until closed.
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