
Start by adding new desktops by dragging and dropping folders on the side bar or use the New Desktop item in the File menu.
Desktops mirror folders on your computer so adding files in Desktops moves or copies files. Likewise, if you change the contents of the folder in the Finder the files will be synched in Desktops.
The side bar can be shown using thumbnails of the desktop, as a list or hidden completely (see the View menu). If you hide the side bar you can open desktops using the Desktop menu.
Desktops can each have their own individual display settings which affect the: background picutre, icon size, text size and others. To edit a desktops options contextual click on the item in the side bar or use the Edit Desktop... item in the Desktop menu.
Desktops can be displayed as a normal window, in the menu bar or covering the Mac Desktop.
Change the mode in the View menu under the Mode item.

Groups help you save space by merging files into single icon which can be navigated without opening new windows or creating folders in the Finder.
Create a new group by selecting some files (except for other groups) and contextual clicking on any of the files then choosing the New Group with... item from the menu. Optionally you can use the Selection item in the File menu if you prefer.
You can drag files onto the group to add them to the group and remove them by dragging files out after you open the group by double-clicking.
Smart Groups are like basic groups in their function except instead of adding files manually you choose a set of critera and files (from that folder only) are added automatically.
For example you can create smart groups by: file types such as images/videos, by name or by specific file extensions (like .download for Safari partial downloads).
Create a new smart group by contextual clicking on the desktop and choosing New Smart Group or by using the File menu item with the same name.
To edit a smart groups critera contextual click on the smart group and choose Edit Smart Group... from the menu.

Containers are like groups which arrange files as a list inside the Desktop to save space or visually organize related files.
Create a new container by selecting some files (except for groups or other files in other containers) and contextual clicking on any of the selected files and choosing the New Container with... item from the menu. Optionally you can use the Selection item in the File menu if you prefer.
Files can be added, removed or arranged in the container by dragging and dropping files like you normally would to move them.
Finally you can change a groups icon size or color by contextual clicking on the container.

In Desktops a folder can be either a normal folder which opens as a new window in the Finder or as a Stack which you can navigate from a popup window in Desktops.
You change the display of any folder by contextual clicking on the folder and checking the Show as Stack item.
In the preferences you can also make all folders stacks by default (this can be changed in the contextual menu later) by checking the Show all folders as stacks box.