Problem with Transitions

Im creating a portfolio site right now in flash and I am wanting to do transitions between pages to make it really smooth. Anyhow, I like the tutorial on it but what about if you use movie clips? how does that work? Because if you want to make an intro for that clip you have to do the intro and the outro on the main stage right? Or am I wrong, I also have a menue which is a seperate clip on this.
Thanks
Fidelity!