That depends on whether there is an automatic layout algorithm involved or not. If not, then you can just move (with your mouse) the target end of an edge to where you want it to attach to the perimeter. For this, select the edge and then move the black square that marks the edge's target end.
If you want an automatic layout algorithm to respect where your edges connect to the nodes, you need to configure this using the Port Constraints tool (under Tools menu > Constraints > Port Constraints). See also: http://yed.yworks.com/support/manual/yed_tools.html
Note, however, that not all automatic layout algorithms support port constraints. This concept makes the most sense for layout algorithms that have a notion of direction / layout orientation. An Organic layout doesn't have this and so also doesn't (in fact, cannot) respect port constraints.
