For extending Soot to use a customized Main class see soot documentation.
Then you need to put your compiled classes (or a symlink to them) in the $ECLIPSE_HOME/plugins/ca.mcgill.sable.soot/ directory and edit the plugin.xml file to include a library tag with the path.
<?xml version="1.0" encoding="UTF-8"?>
<plugin
id="ca.mcgill.sable.soot"
name="Soot Plug-in"
version="1.0.0"
provider-name=""
class="ca.mcgill.sable.soot.SootPlugin">
<runtime>
<library name="soot-plugin.jar"/>
<library name="soot/classes/"/>
<!--<library name="sootclasses.jar">-->
<library name="myclasses/"/> <--add this line
<library name="jasminclasses-sable-1.2.jar"/>
</runtime>
<requires<
<import plugin="org.eclipse.core.resources"/>
...
</plugin>
Alternatively you can add to the plugin.xml an absolute path to your classes directory (I think).
Restart Eclipse. In the Soot Options Dialog there is a page called Soot Main Class. In the text box type the main class you wish to run and the plugin will run Soot with that class.