Hello,
Incompatibilities occur when you have two or more mods that are attempting to override the same file, usually a .2da file. Other files, such as .uti and .utc files, depend on the 2da files for their properties, so if you have to merge two 2da files together, you often have to also modify the files that depend on them.
2da incompatibilities are relatively easy to fix. TSLPatcher does an excellent job of it if the mod was distributed with it.
You could also have a conflict if two mods are trying to override the same template (*.ut*), model (mdl), skin file (tga), script (ncs) or something else. If that's the situation, fixing it is much more complicated, if possible at all. Fortunately that situation is much more rare.
As for FAQs, the closest we have are tutorial forums. You might take a look at the 2da editing tutorial forum (
http://www.lucasforums.com/forumdisplay.php?f=596) to read about how different 2da files work and also look at the general editing tutorial forum (
http://www.lucasforums.com/forumdisplay.php?f=592).
HTH