I have not much experience in web development and I have some problems with action confirmation on my site admin panel. As I know, JS have standard confirmation dialog etc. So should I use this to confirm user action or it will be better to write custom modal window ?
Better to avoid usage alert() prompt() and confirm and use custom dialogs.
There are many libraries that you can use instead of js dialogs (for example: Angular Material or Bootstrap Modals)
Also check this fresh article: Chromium policy on JavaScript dialogs
Did you already check this?