Basically, I have a table that I store all known possible map jumps, even including the unreachable scripts as I have no good logical way to disregard them. Then, I create a new group and manually add any map to it, it will show the map I added as a green node (meaning it's now within the group) and it will also auto add red nodes, which are the known jumps that are possible from that map, then with a series of left and right clicks, I can make any of those red nodes green (adding to the group, and then adding more red nodes off that), and also remove nodes that are definitely not possible ways out of the group (at that moment of the game). This process is also the same for specifying whether it's bidirectional or one way.
And yes, the grouping is manually controlled, meant for segmenting it into portions that a walkthrough may have. It's possible, if I keep the groups small enough, that multiple walkthrough authors can utilize this site to show their walkthrough on, they might combine some of these groups into one paragraph, so two node groups would merge and the site would basically combine the enemy bestiary stats and what-not accordingly.