I can answer your first question, although in brief.
The texture files are saved in ERF -> Texture Packs
The location swpc_tex_TPA.erf holds the highest quality textures (with TPB and TPC in descending order of detail) The exception to this is swpc_gui_.erf which has the Graphic User Interface elements like the player health icons..etc
The other item in the ERF folder is the module files .mod which each contain the .are .git and .pth
(I believe .are stands for area and .pth for path, but .git eludes me...)
And also in the Modules folder is the dialogue for that module, saved as .dlg in dlg.erf
RIMS holds
The .rim files which have inside them the area info files, .git .ifo and .are
The BIF folder holds,
The 2d array files (.2da)
The dialogue files (.dlg)
and the global journal file (global.jrl)
The template files,
Pallete blueprint .itp
Character blueprint .utc
Door Blueprint .utd
Encounter Blueprint .ute
Item Blueprint .uti (heh )
Placeables Blueprint .utp
Triggers Blueprint .utt
Waypoint Blueprint .utw
Letter Combo Probability File .ltr
And List of Soundsets .ssf
Lightmaps.bif (basically used to create artificial dynamic lighting) saved as .TPC textures
<it also contains .viz files which I do not know the purpose of at the moment>
The actual GUI code for the elements which are .gui
Layout files .lyt
Script, both complied (.ncs) and source (.nss)
Sound files in .wav format
And actually, model files are saved under models.bif as two files, .MDL and .MDX The two must both be put into the override to work.
It could take some time , but I could link tutorials for at least the basic file types.
One last thing, the texture files have to be extracted to .tga before you can edit them
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In regards to your second question, the Override folder just replaces the files in Kotors files for whatever is in it, so it isn't necessary to change the filename for them to work. However, conflicts can arise with some filetypes being in the override, such as .mod files, and some files don't work in the override at all (like .wok files, I tried, they just crashed my game) Additionally it is general good practice not to have folders inside the override.