For long distance connections, I often use a pale line if I am in the early stage and will probably rearrange the map later. If the connection will not shorten soon, I often use yellow. Both pale and yellow don't obscure the rest of the map too much.
For arrows, there is no direction that is more correct or intuitive: should it point to the explanation, or should it point to its anchor like the pointed end of a balloon legend? For hierarchical, star-like structures, pointing to the center may be better or worse for legibility, depending on the shape (for Condensr arrows it is better).
For more on legibility, see Shortening and Reading-only.