Here is an update of my B-2 with a stand off missile in the (slightly enlarged) bomb bay. This missile packs quite the punch, one direct hit can sink anything, assuming you can hit the target.

The various systems are operated thus;

AG1 - activates the bomb bay doors. VTOL up opens, neutral closes.
AG2 - activates flaps. VTOL up lowers, neutral raises.
AG3 - lights on / off
AG7 - Drop and activate missile. VTOL up deploys the control surfaces and ignites the engine.

Note: it is recommended that you deploy the missile by;

1 open bay doors.
2 deactivate AG1 and return VTOL to neutral
3 Activate AG7 and VTOL up. This deploys and activates the missile.
4 pilot the missile to target and attack
5 VTOL to neutral plus AG1 to close doors.

Have fun!