First, we should clear up a misconception regarding FPLR (Riser) wiring in a home. FPLR wire is not required to be used in a residence, regardless of the height or size of the home (NEC, 2008, 760.154(b)(3)). A second misconception is that FPLP (Plenum) rated cable is required in a home- it is not. Neither is residential wiring required to be in conduit when passing through the width of an air duct space. This is the logic for that exception: in a home, air for heating and cooling throughout the house is commonly 'ducted' by using the space formed when drywall is attached to both sides of wall studs. Air returns are often made by using sheet metal to enclose the space formed by floor joists and the floor above. If the wooden floor joists caught fire, they would produce much more smoke than the little bit of FPL run through that space, so the FPL is of no consequence. However, the NEC does NOT permit running FPL/CM wiring exposed inside of, or along the length of these air-handling spaces (NEC, 2008, 300.22 (C)). This should never be a problem for experienced technicians since there are so many other spaces and routes available to run wiring inside a home.
Firestopping in a home isn't necessary, or required by code, since homes contain no fire barriers to be penetrated. There are a few other specific wiring rules that need to be followed. Your low-voltage alarm wiring should always be at least two inches away from other 110/220vac wiring in the home to avoid induced voltages and electrical "noise." The two-inch rule doesn't apply to non-metallic sheathed cable (Romex(r)). [This exception, found at NEC, 2008, 760.136 (G)(1) allows you to share the same stud that contains wiring for lights and outlets.]
Good workmanship means you will only drill a hole where permitted (do not weaken framing members) and then only large enough for your cable(s) to pass through without binding or sticking. When running cable along the side of framing members it must be kept back from any edge, at least 11/4 inches. If you notch the wood, the edge of the hole must be made at least 11/4 inches back from the edge, and you must use "a listed and marked" steel plate or sleeve to protect the wiring from nails and screws. These plates are cheap and plentiful from any electrical supply house and using them will keep you on good terms with the drywall contractors.
Following the manufacturer's installation instructions ensures the equipment will be installed in compliance with the codes and standards and operate as required by NFPA 72. Don't miss a chance to keep your local inspector 'in the loop.' You can educate them on code-compliant wiring methods by using your installations as shining examples of proper workmanship.