First thing's first, let's sort out what's displayed where.
BLIZZARD MINIMAP
The yellow exclamation marks (for quests you can pick up) and question marks (for quests you can turn in) pop up when you're 80 yards or less away from the place where they can be accepted or turned in, respectively. This is a confirmed, authentic location, retrieved from the server by Blizzard's UI.
CARBONITE MAP
The parchment symbols (for quests you can pick up) and question marks (for quests you can turn in) appear when the zone in question is in focus. Thus, it is not limited by the 80 yards Blizzard uses. However, they are estimates. The question marks appear where a quest turn-in point
should be. This being said, it doesn't mean it actually has to be there, especially if the NPC that accepts the quest wanders, or if he/she is on some sort of trasnport craft. Also, the parchments that show quest starters are subject to the same wandering / moving NPC irregularity, in addition to only being able to show quests that Carbonite has no recollection of you completing - hence, any quests Carbonite wasn't activated while you did is treated as never completed and thus, available.
The Blizzard minimap can be merged with the Carbonite map (as you know), which causes the Blizzard !'s to seem to appear on top of the Carbonite map. But they can never be shown on the Carbonite map in actuality (until Blizz permits addons to do that, which I doubt they ever will).
Now that that's out of the way, I'll tell you how to show the parchment icons I talked about earlier.
In the Quest Watch window, there's a row of four circular buttons. One of these toggles between three modes (the third one, I think) - faded gold, bright gold, and blue. Blue, of course, represents the daily quests, with their blue exclamation marks, this setting shows only the daily quests on the map. Gold shows all available quests, and is the one you want. Faded gold, naturally, is off.
Hope this lengthy post has been of use to you.