Here are the options for the main configuration screen and an explanation of each of the options. Most options take effect on the next image cycle without a respring but some may require a respring:
BossPaper Enabled - Global enable / disable of the paper theming. If off, all features are disabled and not used.
Solid Colors Only - Enable solid color mode. No images are loaded. You can pick the color using the Color Select section.
Folders - Select the folders you want containing the images you wish to rotate. You can select multiple folders.
Individual Pictures - Select the images you wish to display as individual images. If you want only one image without any rotation, you should select it here and remove any selected folders. Individual images can be used with folders. The folders are scanned first then the individual images added afterwards.
Dock Images - Select the dock style you want. You can also use whatever is in your favorite winterboard theme just apply it in winterboard. If you are using winterboard, this will create a winterboard theme called "BossPaperDock" and apply it for you via winterboard. If you do not have winterboard installed, this will copy the dock image over your original image. Just select Stock iPhone Dock to restore it. Note: if you change this image without Winterboard installed and uninstall BossPaper, you will need to reinstall it and change it back to get the stock dock.
Solid Colors - Here you can select the color you want for your solid background. You cannot rotate this. You must enable "Solid Colors Only" for this to take effect. Make sure you use "Back" when done or the setting will not be saved.
Transitions - Select how you wish the images to transition from one to the next. If you have a slower device (not a 3gs) and you find performance issues or lag, you can disable transitions or determine which transitions perform better. Generally, fade is smoother than ripple on slower devices, for example.
On App Close - Transition to the next image when you exit an app. You can disable the timer this way if you want or run it with the timer as well. Actually changes image any time springboard is shown including after unlock.
Change On Timer - Enable the timer, for use when On App Close is OFF. Recommended use.
Image Rotate Interval - The time between image rotations. If the blue button is 
, you are in seconds, if it is 
you are in minutes, if it is 
you are in hours. Tap the button to change the units. After changing the units, you must move the slider for it to take effect or the change will not be saved.
Transition Length - The time a transition takes. This speeds up the transitions or slows it down. I would try something in the 1-2 second range. Slower devices may want to make this shorter.
Disable Random - Disabling random image rotation puts images in sequential order. This is the order they are added or scanned. This always starts at the first image after respring or reboot.
Dimming - Apply a dimming effect to your images. 1.00 is standard brightness. Smaller numbers equal a dimmer background.
Hide Icon Labels - Remove the springboard icon labels.
Hide Dock Labels - Remove the springboard dock labels.
Under Winterboard - This puts the BossPaper either underneath the winterboard background or on top of the winterboard background (default). When OFF, BossPaper images load over winterboard. If you have a winterboard theme with backgrounds enabled, you won't see the backgrounds. This is useful if you want to show icons from a theme that has a background but let bosspaper show the background. However, lets say you have a desktop widget like a date / time widget. BossPaper covers this. Therefore, you will want to set this to ON in order for the widget to overlay on top of BosPaper. Note that if you do this and have any winterboard themes with backgrounds enabled, BossPaper will not show because it will be covered by them. As a trick you can create or install a theme that has a 320x480 transparent png background image and move it to the to of the winterboard list as active. This will disable all other winterboard backgrounds letting you have your date / time widget with BossPaper backgrounds with other themes that have backgrounds using only their icons.