I'm not sure exactly what you're going for, but I've done something with multiple quests, so I'll explain what I did and maybe that will be of some help.
I have a split in my main quest. The player can choose to do one of two things. However it starts and ends the same way no matter what. So, I have three quests. FSMQ05, which controls the start of the quest, is started when FSMQ04 is completed, and contains all of the objectives; for both player choices. I then have two other quests, FSMQ05A and FSMQ05B; which each control choice A and B with their stages. If the player chooses choice A, I start up quest 05A and set it's stage to 5. That quest then contains all of the dialogue for that decision, and controls the packages of the related NPC's. I did the same for 05B, for if the player chooses option B.
This gives me an easily controlled split in the quest. They break off into two seperate quests that only activate if the player chooses that option (A and B can never both be started). Then it all comes back together in the main quest FSMQ05 for the ending, joining everything back up and starting the next quest. (06)
Hopefully that helps?