I tested this EXACT scenario with the Getting Started Quest during the CK Beta phase.
1) Hellos/Goodbyes ONLY 1 quests H&G's can ever apply at any one time so if you want to be able to have your npcs acknowledge your completed quests you need to do like I do and set up npcs with their own quests that hold "ALL" of their data for every quest they are involved in on this quest then just alter quest stages for the real quest from the dialog quest.
Note: my FO3 mod ended up with 500+ Dialog Quests and they only served just over a 100 Real Quests so its quite a bit of extra work to keep things in line but the overall effect is superior to the default way of doing H&G's.
2) ONLY 1 quests AI Packages can be applied at any one time so any follow/travel/whatever packages gets prioritized and forces the player to complete the quest with the currently running AI package -> AND TRYING TO DO THE OTHERS WILL LEAD TO BROKEN QUESTS !!! so its best to not do this unless absolutely necessary.
----
What I do is I create Hold Out Quest Stages that check if the NPC I want to use is already being used by another quest and if it is then I set the stage to a middle wait her do nothing stage that only checks for if the npc is released by the first quest to be able to continue the second, the dialog I assign to this stage is as generic as possible (as I tend to reuse npcs quite alot) just something like "Lets finish this task first, then we can speak about that issue." generic finish the other thing first stuff.