There is one Carbonite map. Sometimes it's maximized, and sometimes it's minimized (the M key by default toggles it between the two sizes) but it's the same map.There is only one minimap - the one that Blizzard provides, and in which herb and mining nodes, for example, appear as yellow dots. You can dock the minimap inside the Carbonite map, or leave it undocked (check the minimap section of the Carb options, iirc), but either way, the yellow dots only appear on the minimap (because Blizz provides no way for addons or even their own large map to display those dots).
The default (I'm not sure how to change it, or even if you can) detection distance for nodes is 80 yards, so when you get within 80 yards of one, it shows up on the minimap. When you go out of range, it disappears.
FWIW, I don't dock the minimap in the carb map (because I use nUI and there's a place for the minimap built into the dashboard) and when I'm flying around looking for nodes (using Carb's route feature) I watch the minimap and the "crazy arrow" more closely than the routing trail on the carb map. I rarely miss nodes this way. If you're not using nUI, docking the minimap can work well though.
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