To best start answering your questions I would recomend that you take a look at the various tutorial subforums that we have to get a better feel for each of the file types.
To start it off General Tutorials + Tools
should be your first section to browse and really get a feel for. The sticky in this subforum by Darth333 Getting started with modding + List of Tools + downloads
is the most important for answering your current questions.
I would highly recomend that you read through these sections prior to asking for further assistance as alot of these questions get answered in many different ways in these forums and threads. If there is something still confusing you after this we'll be glad to assist with that.
Also each of our forum sections have different functions. "Holowan Labs" -- for general modding questions, best for questions related to file formats and general "How do I's". "Taris Upper City Emporium" -- for mod releases and a place for the end user to provide feedback or ask question regarding a specific released mod. "T3-M4's Astromech Droid Center" -- for asking questions about a specific tool and how to use it or to report glitches with the tool. "KotOR Tool" -- for asking questions about problems with kotor tool or how to do something in there.
Alot of your above questions are better answered in regards to the file formats themselves but there are a couple that are more kotor tool specific. The more specific ones I will attempt to answer.
The Project Manager was/is an in development feature of kotor tool that is designed to make the process of building a large mod project easier when it comes to organizing the files and which files go in which folder.
The Module Editor is a tool that enables you to fully layout and put together an area module with placeables, creatures, and more. This tool also has some bugs and glitches and limitations.