Once you get the correct tech for entering a wormhole, just select the craft you want to enter and rightclick the center of the wormhole. Your ships will move to the center then automatically pop out on the other side (wherever that is). If you are zoomed out you can just rightclick the wormhole again once your ships are in position.
As a sidenote, there is no phase-jump chargeup when using a wormhole. Also I have found that ships stationed around a wormhole sometimes wander into it and teleport to the other side so keep an eye on them.
Hope that clarifies things for you.
