As you two websites are on different drives (E and F), but on the same server (presumably), you can do this by having Publication specific settings within your cd_storage_conf.xml file.

<?xml version="1.0" encoding="UTF-8"?>
<Configuration Version="6.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="schemas/cd_storage_conf.xsd">
  <Global>
    ...
    <Storages TempFileSystemTransactionLocation="F:\Temp" >    
      ...
      <Storage Class="com.tridion.storage.filesystem.FSDAOFactory" Type="filesystem" Id="IISFileSystem" defaultStorage="false" defaultFilesystem="false">
        <Root Path="F:\" />
      </Storage>

      <Storage Type="filesystem" Class="com.tridion.storage.filesystem.FSDAOFactory" Id="Website2_IISFileSystem" defaultFilesystem="false">
        <Root Path="E:\website2" />
      </Storage>
    </Storages>
  </Global>

  <ItemTypes cached="true" defaultStorageId="sqlServer">
    <Item cached="true" storageId="IISFileSystem" typeMapping="Page" />
    <Item cached="true" storageId="IISFileSystem" typeMapping="Binary" />

    <!-- Website 2 Publication specific -->
    <Publication Id="99" defaultStorageId="sqlServer" cached="true">
      <Item cached="true" storageId="Website2_IISFileSystem" typeMapping="Page" />
      <Item cached="true" storageId="Website2_IISFileSystem" typeMapping="Binary" />
      <!-- any other item mappings you need -->
    </Publication>
  </ItemTypes>
</Configuration>

You will not need another Deployer (or Publishing Target) this way.

As you two websites are on different drives (E and F), but on the same server (presumably), you can do this by having Publication specific settings within your cd_storage_conf.xml file.

<?xml version="1.0" encoding="UTF-8"?>
<Configuration Version="6.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="schemas/cd_storage_conf.xsd">
  <Global>
    ...
    <Storages TempFileSystemTransactionLocation="F:\Temp" >    
      ...
      <Storage Class="com.tridion.storage.filesystem.FSDAOFactory" Type="filesystem" Id="IISFileSystem" defaultStorage="false" defaultFilesystem="false">
        <Root Path="F:\" />
      </Storage>

      <Storage Type="filesystem" Class="com.tridion.storage.filesystem.FSDAOFactory" Id="Website2_IISFileSystem" defaultFilesystem="false">
        <Root Path="E:\website2" />
      </Storage>
    </Storages>
  </Global>

  <ItemTypes cached="true" defaultStorageId="sqlServer">
    <Item cached="true" storageId="IISFileSystem" typeMapping="Page" />
    <Item cached="true" storageId="IISFileSystem" typeMapping="Binary" />

    <!-- Website 2 Publication specific -->
    <Publication Id="99" defaultStorageId="sqlServer" cached="true">
      <Item cached="true" storageId="Website2_IISFileSystem" typeMapping="Page" />
      <Item cached="true" storageId="Website2_IISFileSystem" typeMapping="Binary" />
      <!-- any other item mappings you need -->
    </Publication>
  </ItemTypes>
</Configuration>

You will not need another Deployer (or Publishing Target) this way.

(*Obviously you will need to merge the Publication specific settings in to your own cd_storage_conf.xml file, as you will possibly have other configuration items in there.)