Once you have installed the soot-eclipse plugin and restarted Eclipse you must make the menus available by the following:

Select Window -> Customize Perspective
Expand Other option in the tree
Click on soot then OK

Now under the Project menu there should be a Soot section (the menu items may be grayed out at this point)

You must also switch to the Java Perspective in Eclipse:

Select Window -> Open Perspective -> Java

As Soot runs on java classes you must create or import some
Follow the Eclipse guidelines on creating a Java Project found at www.eclipse.org (look for Online Help section)

One note, currently there are problems with the soot plugin in you don't make a src folder in your Java project and instead use the project as the source folder. So don't do this.

Running Soot on all the classes in your project:

First build the classes.
Then select any java file in the project.
The select Project -> Soot and any menu item under
There are currently four:

Create Jimple - creates Jimple files
Dava Decompile - decompiles
Soot Options - opens a dialog box containing all Soot options 
Manage Configurations - opens a dialog where you can create and save, edit, remove and run different configurations of the Soot options

Running Soot on imported folder of classes:

Select any class file. Right click and select Soot -> and any menu item (they are similar to the project menu items)

Select the foler. Right click and select Soot -> Dava Decompile (to decompile all the classes in your imported folder of classes)

Running Soot on Jimple files:

Select the file. Right click and select Soot -> and any menu item (they ar
e similar to the project menu items)

Attributes:
Selecting Output Options -> Output Format -> Jimple File
and under Jimple Annotations Pack: 

Null Pointer Check Options
	-> unselect Disabled 
	-> select Only Array Ref

Array Bounds Check Options
	-> unselect Disabled
	-> select With All

Running this configuration causes a bunch of attribute tags to be generated.
After running open a generated Jimple File and there should be markers in the file indicating attributes.
Mouse over the line in the editor with a marker and you should see a tooltip with the attribute.
Also these attributes tooltips should appear in the original Java source file.

One other note: For long-running memory intensive Soot configurations Eclipse may run out of memory. To handle this start Eclipse with:

eclipse -vmargs -Xmx300M 
