So until I put together a page for the settings, let's point people to this post...
In a perfect world, you would never need the settings page. All of the settings can be filed under the heading "Advanced Settings" (that's a good idea... I'll think about doing that for the next release) and most users will probably be okay with never touching a thing on the settings page.
The first section details the user options (these are different for every user). The width and height settings control the size of the thickbox window when you start PTE. The minimum dimensions are 750w x 550h. The debugging checkbox enables a debugging interface in PTE. Use this when you have a problem you need to tell me about. (Last, but not least, click the "Reset User Settings" button to quickly set 750 width, 550 height, and debugging disabled).
The second section is only enabled for admins and controls what thumbnail sizes are seen in the PTE interface. (A typical wordpress blog will only have 3 -- thumbnail, medium, large -- but other themes and plugins might add others) This lets you hide certain thumbnails you might not care about editing.
Hopefully this gives you the information you need. Let me know if you need some clarification on anything. Thanks for using the plugin!