It's no problem to add custom key-bindings to the predefined key-bindings in Karabiner/KeyRemap2MacBook.
The default method is to create a private.xml in ~/Application Support/KeyRemap4MacBook or ~/Application Support/Karabiner (depending which OS X is installed: KeyRemap4MacBook works in 10.4-10.8 and Karabiner works in 10.9-10.10).
The xml code you have to add to private.xml probably should look like this:
<name>Numpad-0 to Control_L</name>
<autogen>__KeyToKey__ KeyCode::KEYPAD_0, KeyCode::CONTROL_L</autogen>
Reload the xml by hitting the ReloadXML button in Preferences -> Change Key after finishing the modification.
The non-standard way is to edit one of the numerous pre-defined key-bindings located at *.app/Contents/Resources/include/. You also find samples and the symbol_map.xml as well as appdef.xml (which defines apps if you want to restrict the key-binding to special apps or exclude apps) there or in *.app/Contents/Resources/.