Generally a good practice to split circuit into few sections with 0R jumpers. Often makes it easier to debug the design (you can disconnect other parts of the circuit easily). of course using jumpers as a way to handle crossing tracks is also ok.
You only need to remember that 0R jumper in reality doesn not have 0 ohms. In case of small smd's I'd say something like few miliohms. This can make serious difference in some designs. Also - each jumper type has some maximum current it can safely carry (rather large values - something like 1.5-2A for 0805 IIRC)