Newbie needs assistance

The only other thing is, I know you said about the states, but still not sure on "down fading".

Also, the "startup sequence" stage is knocked out, so for the impulse mode sequence, would i want to put that where the note says //what next?

or after the break;

I'm thinking it would be where "whats next?" is. but just want to get that confirmed.

Also, progress report with code!

// The Enterprise
// Author: Nick Gammon
// Date:   27 December 2012

#include <LedFader.h>
#include <LedFlasher.h>

// pin assignments
const byte StrobesPin = 13;
const byte NavigationPin = 12;
const byte DeflectorbluePin = 11;   // PWM
const byte DeflectororangePin = 10;    // PWM
const byte NacellsbluePin = 9;      // PWM
const byte ShuttlebayPin = 8;
const byte DoorsPin = 7;
const byte NacellsvioletPin = 6;   // PWM
const byte ImpulseorangePin = 5;  // PWM
const byte TorpedoPin = 4;
const byte ImpulseredPin = 3;   // PWM
const byte RCSPin = 2; 
const byte CabinPin = 1;

// Faders

//                                  pin           min   max   millis  on?    stop?
LedFader impulseredFader      (ImpulseredPin,      0,   40,  3000,   false,  true);
LedFader impulseorangeFader   (ImpulseorangePin,   0,   40,  3000,   false,  true);
LedFader deflectororangeFader (DeflectororangePin, 0,   40,  3000,   false,  true);
LedFader deflectorblueFader   (DeflectorbluePin,   0,   40,  3000,   false,  true);
LedFader nacellsvioletFader   (NacellsvioletPin,   0,   40,  3000,   false,  true);
LedFader nacellsblueFader     (NacellsbluePin,     0,   40,  3000,   false,  true);

// Flashers

//                        pin          off-time  on-time       on?
LedFlasher strobes    (StrobesPin,        8000,      100,     false);
LedFlasher navigation (NavigationPin,     2000,      500,     false);

// states for the state machine
typedef enum
  {
  initialState,
  wantCabin,
  wantRCS,
  wantDeflectororangeon,     // impulse mode
  wantDeflectorblueon,       //                 warp mode
  wantDeflectororangeoff,    //                 warp mode
  wantDeflectorblueoff,      // impulse mode
  wantNacellsvioleton,       // impulse mode
  wantNacellsblueon,         //                 warp mode
  wantNacellsvioletoff,      //                 warp mode
  wantNacellsblueoff,        // impulse mode
  wantImpulseredon,          // impulse mode
  wantImpulseorangeon,       //                 warp mode
  wantImpulseredoff,         //                 warp mode
  wantImpulseorangeoff,      // impulse mode
  wantShuttleBayopen         // open in impulse 
  wantShuttleBayclosed       //                 closed in warp
  wantNavigation,            // ALWAYS ON
  wantStrobes,               // ALWAYS ON
  wantTorpedoon,             // impulse mode
  wantTorpedooff             //                 warp mode
  
  // more states here
  
  } states;

// state machine variables
states state = initialState;
unsigned long lastStateChange = 0;
unsigned long timeInThisState = 1000;

void setup ()
  {
  pinMode (CabinPin, OUTPUT);
  pinMode (RCSPin, OUTPUT);
  pinMode (ShuttlebayPin, OUTPUT);
  pinMode (NavigationPin, OUTPUT);
  pinMode (StrobesPin, OUTPUT);
  pinMode (TorpedoPin, OUTPUT);
  pinMode (NavigationPin, OUTPUT);

  // set up faders, flashers  
  impulseredFader.begin ();
  impulseredFader.begin ();
  deflectororangeFader.begin ();
  deflectorblueFader.begin ();
  nacellsvioletFader.begin ();
  nacellsblueFader.begin ();
  strobes.begin ();
  navigation.begin ();
  }  // end of setup

        
void doStateChange ()
  {
  lastStateChange = millis ();    // when we last changed states
  timeInThisState = 1000;         // default one second between states

  switch (state)
   {
    case initialState:
         state = wantCabin;
         break;
         
    case wantCabin:
         digitalWrite (CabinPin, HIGH);
         state = wantRCS;
         break;
         
    case wantRCS:
         digitalWrite (RCSPin, HIGH);
         state = wantDeflectororangeon;
         break;
         
    case wantDeflectororangeon:
         deflectororangeFader.on ();
         state = wantDeflectorblueon;
         break;
         
    case wantDeflectorblueon:
         deflectorblueFader.off();
         state = wantNacellsvioleton;
         break;
         
    case wantNacellsvioleton:
         nacellsvioletFader.on();
         state = wantImpulseorangeon;
         break;
         
    case wantImpulseorangeon:
         impulseorangeFader.on();
         state = wantShuttleBay;
         break;
         
    case wantShuttleBay:
         digitalWrite (ShuttlebayPin, HIGH);
         state = wantStrobes;
         break;
         
        case wantStrobes:
         strobes.on();
         state = wantNavigation;
         break;
         
    case wantNavigation:
         navigation.on();
         state = wantTorpedo;
         break;
         
    case wantTorpedo:
         digitalWrite (TorpedoPin, HIGH);
              

         timeInThisState = 5000;         // no rush

         // what next?
         break;
   
   
   }  // end of switch on state
    
  }  // end of doStateChange


void loop ()
  {
  
   if (millis () - lastStateChange >= timeInThisState)
     doStateChange ();

   // update faders, flashers
   impulseorangeFader.update ();
   impulseredFader.update ();
   deflectororangeFader.update ();
   deflectorblueFader.update ();
   nacellsvioletFader.update ();
   nacellsblueFader.update ();
   navigation.update ();
   strobes.update ();
 
  // other stuff here like testing switches
    
  }  // end of loop

The notes in the want list are there to help me keep organised, so pay them little mind.