You would need a FSD wake scanner to follow them between systems. Your best bet is to go to an anarchy system and park at the nav beacon and scan ships as they pass through, you'll find plenty of targets. Extraction sites are another good hunting ground as pirates love to go after miners.
I've had poor luck with the wake scanner. I thought it would give you a good trail on them and basically send you 'close' enough to them to see them so you could interdict all over again. No such luck, the thing just warps you to the system, good luck finding a single ship in a system when they have a lead on you. Though most of the time since I'm in a small fighter (eagle atm) I can't even get to the system that they jump to. I guess later on when I can afford a ship that can actually carry a wake scanner and a kill warrant scanner and a good jump distance it might come in more handy than it does in the early game.
I wish there was a more reliable way of knocking a ship's engines out. I've tried concentrating fire on them but most of the time it's quicker just to wax the whole craft.
Bounty hunting is a tough life.
Also, if you're careful (and brave or stupid) you can get away with killing folks in 'clean' systems with a warrant in another system. If you just get the hell out of dodge quickly. Also, if the popo show up just press that middle finger up against the glass and fire up the friendship drive. POOF
I love this game so much.