GuardianLurker
Adventurer
Don't Panic
Others have answered your exact questions fairly well; I'm not going to try to better them in the specifics.
Overall general advice :
1) Don't Panic!
When your players kill the NPC you had intended to be their arch-nemesis, Don't Panic! Let them. You can always reuse the NPCs stats, and probably most of the Backstory as well.
When your players miss that subtle clue, or do something that completely demolishes the plot of the adventure, Don't Panic! Let them. There will be other adventures, and you will find that they can often be easily sidetracked into something minor that lets you scramble to get the next thing in place.
2) Be adaptable.
No module, no adventure, no plan of the GMs survives contact with the players. No matter HOW much you prepare, you'll always have to "wing it" at some point. Balancing this, your players will generate some of your best ideas - listen to their chatter and use it.
Players are both geniuses and complete and utter idiots. They're Murphy's Law incarnate. (And I speak as both Player and GM here.)
3) Never forget the 7Ps : "Proper Prior Planning Prevents Piss Poor Performance"
Especially in the beginning, plan and prepare more than you think you will need to. Somethings you won't use, others you will forget. Change. Over time, you'll discover what the proper amount of preparation for you is.
Honestly, the various tricks work well to solve the mechanics, but it's the attitude you bring to the sessions that makes all the difference.
Others have answered your exact questions fairly well; I'm not going to try to better them in the specifics.
Overall general advice :
1) Don't Panic!
When your players kill the NPC you had intended to be their arch-nemesis, Don't Panic! Let them. You can always reuse the NPCs stats, and probably most of the Backstory as well.
When your players miss that subtle clue, or do something that completely demolishes the plot of the adventure, Don't Panic! Let them. There will be other adventures, and you will find that they can often be easily sidetracked into something minor that lets you scramble to get the next thing in place.
2) Be adaptable.
No module, no adventure, no plan of the GMs survives contact with the players. No matter HOW much you prepare, you'll always have to "wing it" at some point. Balancing this, your players will generate some of your best ideas - listen to their chatter and use it.
Players are both geniuses and complete and utter idiots. They're Murphy's Law incarnate. (And I speak as both Player and GM here.)
3) Never forget the 7Ps : "Proper Prior Planning Prevents Piss Poor Performance"
Especially in the beginning, plan and prepare more than you think you will need to. Somethings you won't use, others you will forget. Change. Over time, you'll discover what the proper amount of preparation for you is.
Honestly, the various tricks work well to solve the mechanics, but it's the attitude you bring to the sessions that makes all the difference.