Waterproof/breathable jackets have two types of waterproofing. The main waterproof layer is a membrane (gore-tex, gelanots, e-vent et.c.) which doesn't allow water to pass through the jacket, even if it is soaking in to the outer fabric. The second type is a DWR (durable water repellant) coating on the outer fabric of the jacket. This DWR coating is what breaks down/wears off over time and needs replacing. You'll know it's time to re-coat the outer of your jacket when the water starts soaking in instead of beading and rolling off.
As long as the jackets waterproof membrane is still intact it should stop any water from coming right through the jacket. What will start happening once the DWR layer breaks down/wears off from the outer is water soaks in to this outer fabric and stops the jacket from breathing. Although it will still keep the rain out you will notice the jacket starts to feel clammy on your skin as a result of the water sitting in the outer fabric and your sweat not being able to escape (i.e. no longer breathable).
Washing and drying your jacket
Before you spray your waterproof jacket with a water repellant spray it is important to ensure the jacket is clean. The best thing to do is follow the washing instructions printed on the jacket. If these are not present or are unreadable the best thing to do is to hand wash your jacket using a mild soap (e.g. nikwax tech wash) and warm water. Do no use detergent unless the jackets instructions specify that you can!
If particular patches of your jacket require special attention you can spot clean them using a cloth or giving them a gentle scrub with a brush if needed.
Once your jacket/pants is clean you can generally put them in the dryer on low heat, however, only do so if the washing/drying instructions recommend this! If the instructions say do not tumble dry or you are unsure then leave the jacket to dry naturally.
Reproofing your jacket
The spray you buy to reproof your jacket (e.g. Gecko Guard or Nikwax TX-Direct) should come with instructions on the bottle. The following steps are a general guideline.
1. Shake bottle and spray the jacket evenly with a slow sweeping motion from about 20cm away, until the fabric is completely covered with a light coating. Over applying will not improve results.
2. Leave the jacket to dry naturally or use a dryer or cool iron if care instructions allow. Left to dry naturally with spray will take 48-72 hours (depending on conditions) to cure completely.
3. Once dry test for water repellancy by splashing or spraying with water. The water should form beads and roll off. Depending on the state of the waterproofing prior to treatment you may need to apply a second light coating. If the water is not beading a rolling off effectively thenn repeat these reproofing steps.