When reading my tutorials and explanations about SB3Utility (abbreviated SB3U / SB3UGS) some terms are important to recognize. Many 3D programs use the same terms with an other meaning and that's why I define even the simplest terms here. If something is related to one company only it is written in the following colour schema: Illusion, Tea Time, REAL.

Vertex
A vertex consists of
  • a position in 3D space with X, Y and Z coordinates,
  • a Normal also with X, Y and Z coordinates which is used for lighting,
  • a 2D coordinate pair UV which defines a point on a Texture,
  • upto four references to Bones and Weights used for animation. All these fields are empty for unskinned Meshes/Submeshes.
    Although the same fields are present in an ODF, all used skins are stored in a seperate section (ENVL). REAL doesn't even have these fields in the vertex structure and stores it in the SKIC section.
Normal
Normals exist in two flavors. In Sb3U only vertex normals are visible in the renderer and are referred to in dialogs. They are not present in MQO files and must be computed by Sb3U. Three vertices build a face which are used to compute a face normal. The adjacent faces have common vertices. The vertex normal is computed as a sum of all face normals. Faces that the vertex is part of. Because of the order in which the vertices are considered the vertex normal points in a direction which is defined as outward.
Sb3U shows the difference when you look at the face from the other side. If Culling is active, then the face is invisible. Switching off Culling shows the face regardless of position and direction of the camera. The renderer has an option to display vertex normals.

UV
They are also called texture coordinates, which define a point in 2D space on an image. They are found in MQO files at the definition of the faces. Three UVs because of the three vertices per face. Metasequoia would store more (and more vertices per face), but the games need triangulated faces and Sb3U displays error messages when importing faces with more than three vertices.

Submesh (Mesh Object)
Submeshes have a list of vertices and faces, can be switched off with the unknowns, and can use one Material. They are always contained in a Mesh. ODFs store references to Textures here.

Mesh
A mesh is a container for Submeshes, can also be switched off with it's unknowns and has a special form of vertex list called the Duplicate Vertex List. Most importantly it hangs in a Frame which is called Mesh Frame. The Bone List is also kept here.

Frame
A frame is part of a hierarchy with each node being a frame. This hierarchy is shown in Sb3U in the Object Tree. Each frame has a transformation matrix which deforms everything below the frame. And below means the children of this frame: meshes and other frames. The transformation matrix defines translation, rotation and scaling. Being part of a hierarchy means, that each child receives the transformations from it's parent, grand-parent, grand-grand-parent and so forth until the Root Frame is reached.

Bone
Bones used by all mesh objects are kept in a list in the mesh. In ODFs each mesh object has it's own bone list. They reference a frame called Bone frame. Each bone has a transformation matrix which is usually additionally applied to each animation. If no animation is used then the transformation matrix defines the Rest pose. Selecting a bone in the object tree highlights that bone.

Material
The properties of materials change how the used Textures look. In XX units references to Textures are stored here. ODFs can include several property sets for a material.

Texture
A texture is an image, which is stored in a pp file, then you find the texture in the Img tab. Or it can be stored in a XX unit and you can select it in the Texture tab. ODFs store only their name; the image itself lies in same folder as the ODF. Selection is the same as if it would lie in a XX unit.

Animation Track
An animation track is a container for every change of a bone over time. And such a change is called keyframe. Illusion puts several animations for a character one after the other by appending the keyframes to the same track.

Animation Clip
An animation clip just says where one single animation starts and ends and at which speed the animation should be played.

More useful information:
darkhound's explanation about the workspace's copy modes.