Yeah, when assembling the map so far, I've decided that some of the encounter sets will be 'basic,' with no attached quest, while others will need to have their quest (or a shortened version) included. Return to Mirkwood, for example, has numerous references to Gollum, which means that you would have to include that quest (or preferably a shortened one-quest-card version with maybe 12 progress required and directions that you have to guard Gollum).
However, I think that many of those special quests could be 'overlays' on the existing map. For example, the entire Mirkwood forest is already covered by these three sets: Passage Through Mirkwood (west portion of Mirkwood), Spiders of Mirkwood (east portion of Mirkwood), and Dol Gulor Orcs (central to south portions of Mirkwood). Return to Mirkwood seems like it would be an add-on quest that you could choose to do instead of one of the others (or in addition to those), for bonus points.
Marking up the map has been fun so far. I take a Middle Earth map and draw a shape that encompasses all the locations in an Encounter Set. Then I do it again for the next encounter set, and again for the next, modifying each as I draw them so that they will not overlap. I couldn't get Return to Mirkwood not to overlap with the 3 sets I mentioned above, but I figure that that set needs a quest card anyway, so it can be an overlay.
So far I have completed the Core set and the Shadows of Mirkwood cycle.
I'm about to venture into Moria. I'm not sure what I will find...