If it were me, given the little bit of info you have just provided, and assuming that the BBEG's know what their opponents look like and have ample resources at their base of operations, I'd first have them hire out urchins to keep an eye out for the PC's and let the bad boys know when they get into town. Then I'd have the baddies get an NPC close to the group, perhaps a hooker, or even another saavy urchin to gain thier confidance and "help" them in this big unfamiliar town they are now in. Once you have an insider, you can keep the bad guys up to date on the PC's actions and movements, maybe even their plans if they trust the mole enough. From there it shouldn't be hard to set up ambushes, poison attempts, assassinations, etc. Eventually they need to come across someone who knows something about these operatives so that the PC's can get on the trail. Perhaps a servant who learned too much and is now in hiding from the bad guys because they want to kill him for konwing too much learns of the PC's snooping and drops some info their way in the hopes that the PC's take out his former masters. Or perhaps a spy of the King notices the PC's and decides to use them as pawns to get into the bad guys base of operations and arranges the PC's to come across location info... lots of possibilities here.