These are answers to some of the most frequently asked questions. Read these before asking a question here.
Furthermore, a list of common bugs (and how to avoid them!) can be found here:
http://nifflas.lpchip.nl/index.php?topic=2427.0Q: How do I place objects?A: Select layer 4, 5, 6 or 7 to place objects. Select layer 0, 1, 2 or 3 to place tiles.
Q: Juni keeps falling through the floor. How can I place walls/floors?A: Select layer 3 to place tiles which Juni will collide with.
Q: How do I make signs/shift objects?A: You can configure those with the Knytt Stories Manager, which can be found here:
http://nifflas.ni2.se/forum/index.php?topic=17.0 (or with version 1.0.2 and up of Knytt Stories)
Q: The Knytt Stories Manager crashes when I start it!A: Make sure it's placed in Knytt Stories\3rd Party Tools\KSManager\. You'll have to create the folders yourself. If you still can't get it to work, download the latest version of Knytt Stories. It's included there.
Q: When a cutscene is over, I go back to the last savepoint!A: Turn on ShiftSave(A/B/C)=True (or Autosave Game in the KS Manager), so the game is saved to the target location.
Q: But I don't want to use the KS Manager, is there no other way? 
A: Sure, tipps on modifying the .ini without the Manager are to be found
here.
Q: I want to add/edit something small about a tileset I found, but I can't find the original author to ask them for permission! What do I do?
A: Read
this.
Here's a list of very very helpful topics on the...topic.
Manuals/Tuts:
http://nifflas.ni2.se/forum/index.php?topic=18.0 (PDF-Manual)
http://nifflas.ni2.se/forum/index.php?topic=19.0 (Tutorial Videos)
http://nifflas.lpchip.nl/index.php?topic=20.0 (Cutscenes Seminar)
http://nifflas.lpchip.nl/index.php?topic=1742.0 (Simple Tileset tut)
You can download a special level with a demonstration of all advanced features here:
http://nifflas.ni2.se/forum/index.php?topic=29.0