The banner sideboxes can be cloned once you understand a bit more about what they do ...

For example ...

/includes/modules/sideboxes/banner_box2.php
/includes/templates/template_default/sideboxes/tpl_banner_box2.php
are clones of:
/includes/modules/sideboxes/banner_box.php
/includes/templates/template_default/sideboxes/tpl_banner_box.php
The differences that allow them to pull their own set of Banner Group banners are the settings in the Layout Settings where the Banner Groups are defined for each banner sidebox ...

The banners_box uses the Banner Group names defined in:
SHOW_BANNERS_GROUP_SET7

To know which banners to look for to be displayed ...

The banners_box2 uses the Banner Group names defined in:
SHOW_BANNERS_GROUP_SET8

To know which banners to look for to be displayed ...

To clone this for another banner sidebox, you would need to create copies for the 2 files for banners_box2 and modify them by copying to:
/includes/modules/sideboxes/banners_box3.php
/includes/templates/template_default/sideboxes/tpl_banner_box3.php
This would require its own unique setting for which Banner Groups to include, such as creating a new configuration_key for:
SHOW_BANNERS_GROUP_SET10

Why use SHOW_BANNERS_GROUP_SET10? Because it is unique and has not been used before ...

This could be added to the configuration table like the other Banner Group definitions, or it could be added to a define statement ...

Extra define statements are best added to the directory in a file that has meaning to you such as:
/includes/languages/english/extra_definitions/my_banners_box3.php

<?php
define('SHOW_BANNERS_GROUP_SET10', 'BANNER GROUP NAMES GO HERE');
?>

This would load at the same time as the english.php file ...

Or, you could add it to the configuration table in the same way all the other settings are added:
PHP Code:
INSERT INTO configuration (configuration_title, configuration_key, configuration_value, configuration_description, configuration_group_id, sort_order, use_function, set_function, date_added) VALUES ('Banner Display Groups - Side Box banner_box3', 'SHOW_BANNERS_GROUP_SET10', 'SideBox-Banners', 'The Banner Display Groups can be from 1 Banner Group or Multiple Banner Groups<br /><br />For Multiple Banner Groups enter the Banner Group Name separated by a colon <strong>:</strong><br /><br />Example: Wide-Banners:SideBox-Banners<br />Default Group is SideBox-Banners<br /><br />What Banner Group(s) do you want to use in the Side Box - banner_box3?<br />Leave blank for none', '19', '73', '', '', now()); 
Then, you customize the new files for banners_box3 to use the changes described above ...

Example:

SHOW_BANNERS_GROUP_SET8

would become:

SHOW_BANNERS_GROUP_SET10

TEXT_BANNER_BOX2

would become:
TEXT_BANNER_BOX3

PHP Code:
    require($template->get_template_dir('tpl_banner_box2.php',DIR_WS_TEMPLATE, $current_page_base,'sideboxes'). '/tpl_banner_box2.php'); 
would become:
PHP Code:
    require($template->get_template_dir('tpl_banner_box3.php',DIR_WS_TEMPLATE, $current_page_base,'sideboxes'). '/tpl_banner_box3.php'); 
etc. etc. etc.

NOTE: The new defines can also be included in your new file:

/includes/languages/english/extra_definitions/my_banners_box3.php

to keep everything related together ...

Hope this can help give you a start on making new banner boxes ...