Each payment method that extends Mage_Payment_Model_Method_Abstract
has the following member variables:
protected $_canUseInternal = true; //can use in admin
protected $_canUseCheckout = true; //can use in onepage checkout
protected $_canUseForMultishipping = true; //can use in multishipping
As shown above they are default 'true'.
If you want to use a method only for admin override their values in your payment model as follows:
protected $_canUseInternal = true; //can use in admin
protected $_canUseCheckout = false; //can use in onepage checkout
protected $_canUseForMultishipping = false; //can use in multishipping
Then enable the method from the system->configuration->payment methods section.
It shouldn't appear in the frontend (but test it in case I'm wrong) but you should be able to see it in when creating an order from the backend.