The theme system may look complicated but its quite easy to learn to use and is really powerful to use (you can pretty much move away from the MyBB look by editing it and nothing else).
A small overview on the various sections in the themes editor is as follows:
(This just the majority of the items - the rest you should be able to work out).
Now, when editing each of those you'll notice a fairly standardised set of options:
Background - allows you to specify the background colour (or image) for that specific element.
Font Colour - allows you to change the font colour for that specific element.
Font Family - allows you to change the actual font that is in use for that element.
Font Size - allows the font size to be customised for that element.
Font Style - allows text to be italicsed or similar for that element.
Font Weight - customise the "width" or "boldness" of the text.
Extra CSS - this allows you to enter any additional CSS that you wish to for this item.
Links - you can customise the background colour, font colour, and text decoration (under the text) for normal, visited, and hovered links.
(However this changes for some different elements because of the nature of them).
The way the theme system works is based on inheritance. Themes can have an unlimited number of parent themes (although the top-most parent can only be the Master Style) and any themes who do not have a customised value in those sections will inherit that class/element/selector from the themes parent.
Basically this means I can create a fixed and liquid width layout of MyBB quite easily, I just make another theme and set its parent to "MyBB Default", and change the forum width. The rest of the information is inherited whilst the forum width is the only customised item in that theme.
The Master theme is there to serve as a backup incase everything else fails, and to provide a top level of inheritance. You should not edit this theme (and that will be infact disabled in 1.0 - apart from editing the master css for it) because its what we'll use when we need to add new classes and areas to the themes manager - we'll overwrite it.
Themes also work along side with CSS inheritance - if you leave a value blank in one of the sections then CSS will automatically inherit it from its parent object (most likely the body).
If at any time you've customised an area of a theme and you wish to completely revert it, you can check the "Revert Customisations" checkbox for the element you'e customised and click Save Changes. It will then revert to its inherited or default value.
Hopefully thats a little bit of an overview, let me know if you need anything else.