Lovely map!
I would NOT color the original. If you're going to continue to work by hand, take it to a copy shop and have several copies made. Use each one for different info. On one, draw cities, towns, roads, borders, that sort of thing. Political info. Maybe several of these for known and unknown political groups that have different types of control (religious vs secular vs the dragon vs the wizards guilds)
On another, indicate natural resources, unusual geographic features, etc...
Maybe you want to color one with land heights - ie coastal lowlands, interior highlands, mountains, hills, etc... and a second with plant cover - ie plains, forests (deciduous vs evergreen?), saltwater vs fresh marshes, and all sorts of other stuff.
And then you could have a map with climate zones and weather patterns. Where are the monsoons, the hurricanes, the tornado zone, and where do earthquakes happen?
Ooops, can you tell I love to draw maps?