You actually don't have to have TomTom installed for other addons to use TomTom, ummmm, waypoints, I guess you'd call them. I have Archy (for archaeology) installed, and Carbonites TomTom emulator enabled, and Archy uses Carbonites HUD arrow and map goto's to point me to my archaeology dig sites.
As far as farming routes go, you can use Carbonite itself to route you around a zone as long as you are tracking that skill through the Blizzard tracking facility (the magnifying glass minimap icon). You can also make your own routes for other things using the "Favorites" feature in Carbonite. One caveat to that, though, is that in order to see the "gold active node icon" on Carbonites map, the maps must be merged. The other is that Carbonite will only route you through node points that it already "knows". However, if you harvest a node previously unknown by Carbonite, it will "remember" that location. Currently, there is no other addon that Carbonite can obtain information from as far as gathering information goes. Also, merging the Blizzard and Carbonite maps is the only way you can see the "active node icon" on Carbonites minimized map since that information is not, as yet, available to addons.
There are a couple of threads in the old (archived) Carbonite forums that explain how they work:
Routing Gathering Nodes, and
How To Route Favorites
Just to ensure that you are aware: Cartographer (the addon) is dead. It hasn't been updated since, I think, WoW 3.something or other. Emulating Cartographer in Carbonite is, probably, pretty useless.
The other thing is that Carbonite can merge the Blizzard Minimap with its' own map, but does not do anything with Blizzards World Map, except open Carbonites maximized map instead of opening Blizzards World Map when the "M" key is pressed as long as that option is checked in Carbonites options (which, according to your first screen shot, it is not in your Carbonite installation).
I highly recommend going to your "
Path to your WoW folder\Interface\AddOns\Carbonite\" folder and reading through the "CarboniteReadMe" plain text file. It explains a lot about what Carbonite is, and what it can do, but it also explains how it can be set up. There is a large amount of installation information at the beginning of the file, but since you already have it installed I think it's safe to skip that part. 8^)