It is healthy to use engine braking on a semi-frequent basis.  Engine braking is required for proper setting of ringlands on a newer engine, since you can't put as much load on the car from acceleration.  Engine braking in and of itself isn't harmful to your engine at all, it is harmful to your driveline especially if you don't know what you are doing.  Your transmission is what is taking the force from engine braking, however, just trusting your brakes is not a good idea.
 While you shouldn't always use engine braking, you definitely need it in some situations and it is something that you want to use occasionally regardless.  If you are coming from a high rate of speed to a stoplight, from an expressway for example, the heat generation from your brakepads will cause them to completely fade out unless you are using high quality pads.  Engine braking is necessary to ensure you aren't overheating your brakes and to give you a proper stop time.
As for Heel-Toe Shifting, for the average clutch driver it isn't necessary.  When you downshift you are being somewhat rough on your transmission, but it is what they are designed for.  They design transmissions to take a little punishment.   The best reason to use heel-toe shifting or rev matching is for downshifting in a high performance car that has a lot of ponies.  If you don't downshift properly, you can torque shock your transmission and greatly reduce the life of the synchros.  But that is only in certain situations and for the most part it isn't that bad, and I am talking only in cars that are really pushing a lot of power, like 350-500 whp.
The only time it is necessary to heel-toe is when using a dogbox, or straight cut gears.  The gears won't line up without rev matching.