Here are some FAQ and answers to them. Most of answers also contain video version. I know my spoken english isn't flawless, but hopefully you will understand me.
IMPORTANT!: While SDL 1.4 is the last public nonBeta release, its over 2 years old. Nearly all issues Noggit has (especially those in FAQs below) are simply no longer present in newer versions of Noggit. If you really don't want/have to use this ancient version, get your hands on as new Noggit version as possible. You can find 3.1408 in my tutorial pack on MC-Net, or get even newer ones from whoever who has a compiled version from repo (if you can't compile that thing on your own).
1. My Noggit crashes/closes itself when I try to run it.
Short answer: Make sure your noggit.conf isn't named noggit.conf.conf, that you have entered correct paths into it and that paths to folders end with . Also be adviced that Noggit is compatible only with WotLK 3.3.5a. However, maps made in Noggit for 3.3.5a can be converted to newer expansions.
2. My Noggit lags very hard and/or I have troubles with bugging selecting models.
Open log.txt and check if your Noggit isn't running on Intel HD Graphics chip. If it is so, go to your 3D graphics settings and make Noggit use your stronger (gaming) graphics card.
3. I can't paint textures in some areas.
Every chunk (red square in grid toggled on by F7) can contain up to 4 different textures. You can use only those 4 textures there. If you want to use another one, you need to replace some of those 4 by your new one via texture swapper, or you can texure that chunk again.
4. When I try to acces my map in game, I get crash.
There can be several possible reasons (for instance corrupted model which you spawned there and so on), but the most common one is marked with code 0023:007B31F8. This error happens when ADT which contains less than 4 textures on some chunk is saved in Noggit. Such ADT might start crashing in game. Filling all chunks with 4 textures is a way around which prevents this from happening.
5. After saving in Noggit, some my models disappear/are duplicated.
All ADTs which contain same models should be always saved together, if you want to modify them. The best way to achieve that is simply always saving a whole map together (for smaller maps) or a whole edited area together (for bigger maps, for instace modified zones of blizzlike world). You should also always restart an application after each save. Because of problem #4 mentioned here, I suggest you to not keep ADTs which are saved by Noggit around ADTs you have directly edited, because they may start crashing and to prevent that, you need to apply 4 textures on them (which means editing them, and that spreads your area which you are modifying, and thats NOT something you want to do in this case).
6. Water disappears from my map when I save it in Noggit.
This should not be a common problem anymore, because it happens only with older versions of Noggit which can't save water (or can't do so properly). Download the newest version (1.4 SDL and newer).
7. Random holes are appearing across my map.
Never click into/drag across holes or gaps in terrain. Use Fix gaps (all adts) function in Assist menu to close gaps and be careful when working around holes created by hole tool. You may want to close holes while working around them and re-create them when you are done with your terrain around them. However, hole creating tool commonly creates 2 holes, one where mouse cursor is, one somewhere in front of you behind place where hole should have (only) been. In such case just turn models off (F1, F6) and close manually holes which were done unintentionally.
8. Some models on my map are invisible in Noggit, what to do?
If you want to just delete those models, there are more ways of doing so, but the only feasible way how to be able to place/move/scale/rotate those models is just swapping invisible model (usually some particle emitter) with some visible model. By doing so, you will see your placeholder in Noggit instead of invisible one, which will enable you to do whatever you want with that model. A video tutorial how to do that without messing around directly in ADT file's structure (which isn't very noob friendly and can corrupt your files if not done properly) follows.:
