In your system.xml you can add Form-Elements. There are 3 relevant nodes:

• frontend_type - corresponding to /lib/Varien/Data/Form/Element
• source_model
• backend_model

I know that you can build your own source- and so I believe backend_model. It is relative easy to do it. Just add the classpath to your nodevalue like "adminhtml/system_config_source_yesno".

If you have a look to /lib/Varien/Data/Form/Element, you can see File.php which you can use to build the Upload-Frontendtype.

For system=>configuration:

In your system.xml you can add Form-Elements. There are 3 relevant nodes:

• frontend_type - corresponding to /lib/Varien/Data/Form/Element
• source_model
• backend_model

I know that you can build your own source- and so I believe backend_model. It is relative easy to do it. Just add the classpath to your nodevalue like "adminhtml/system_config_source_yesno".

If you have a look to /lib/Varien/Data/Form/Element, you can see File.php which you can use to build the Upload-Frontendtype.

For other admin-sections:

You can use extend Mage_Adminhtml_Block_Widget_Form and Hmx_Incopay_Block_Widget_Container

In your widget form you can add the following in the constructor:

$form = new Varien_Data_Form(array(
                                    'id' => 'edit_form',
                                    'action' => $this->getUrl('*/*/edit', array(
                                            'id' => $this->getRequest()->getParam('id')
                                    )),
                                    'method' => 'post',
                                    'enctype' => 'multipart/form-data'
                                 )
    );

and

$fieldset->addField(Mage::getStoreConfig('XXXX/input_file_name'), 'file', array(
            'name' => Mage::getStoreConfig('XXXX/input_file_name'),
            'label' => __('CSV account data'),
            'class' => 'required-entry',
            'required' => true,
    ));

Dont change the form-id and beware of some other conventions listed here http://blog.kervinramen.com/2012/10/how-magento-widget-form-container.html