There really isn't all that much finesse to it. The most important part is to remember to have all your ships trained to cut your own response time. The NRP always reacts quickly and I may be wrong, but their own shock effect may be lasting less than that of the player (usually less than 30 seconds) so you have to be able to fire as quickly as possible.
As for a more advanced advice, I don't think there is any to give really. The enemy will likely be using squadron transit, but the exit point is totally random, so having your ships in a central location, right on top of the jump point, gives you the highest chance of being able to zone on him and that is the tactic I myself have used. If you don't mind splitting your forces you could increase the chance of intercepting incoming enemies by having your own ships form a ring around the jump point, preferably close enough that your missiles arrive within a single five second interval (as this will make them impossible to intercept with the exception of CIWS) but this will leave your own force scattered. In the end aside from sitting on top of the jump point with highly trained and quickly responding forces, I'd say everything else is a matter of luck, as the exist point is random.