How do I make to put a pop-up message but to appear only once? Like I just came in the room for the first time and what is there is an important part of the story.

There is a 'After entering the room for the first time' section of the scripts tab of the room object where any scripts will only be run that first time, otherwise you can always add an attribute to the object such as FirstTime and set this at the end of your story event, then surround your event with a check
IF (FirstTime = False) {
Your story event
}
Else {
Other event
}

take a look at this post of mine (and if interested the entire thread too, but it's topic isn't quite the exact same as yours):

http://textadventures.co.uk/forum/quest/topic/_khselnx50wl-vxz-pppxw/problems-repeating-verbs-commands-resolved#3f22fb3a-8ed9-4a97-a166-878fe4bb9ed8

basically, you need some form of a condition/control, to limit/control it.