For your flaps, please see this thread:
http://www.rcuniverse.com/forum/m_11...tm.htm#1146088
As far as your nosegear is concerned, put your rudder servo on channel 4 as normal. Program the steering servo channel (7 or 8) on a PMIX to be activated by the retract switch so that the mixer is on when the retract switch is in the gear-extended position. Your mixer would have channel 4 as master and the steering servo channel as slave.