When I try to change something (name, or a new application), the new small window to do this appears behind the windows LiberKey. What should I do to this little window appears over the window LiberKey?

Hello and welcome on forums.

Perhaps are you using windows XP.

With it, it appears that some liberkey's menues pop under, but as vagabond has explain here it isn't a liberkey problem but a Windows XP problem.
You can try top apply his solution, or sometimes closing the windows' session and restart another one can solve these.

JP4U