Don't understand your first question, not clear exactly what you mean.  A screencap will help.

If you are referring to adding runtimes to the library, there is a built-in script which will scan your drives and add them automatically. 

Delete library button found upper right hand corner of Library.

No, you cannot use dynamic clothing without running animation. And no you cannot conform it within Poser.  If you are only interested in rendering, select that particular frame.  You can save the posed item as a prop into your library, but it will have restricted functionality.

You can zoom in Poser using the magnifying glass located on the workspace.  But I don't understand what you mean by box or square?

Reversing coloring can only be done with the undo.

Other answers, I'll defer to others.