So you bought a waterproof jacket, now here's how to get the most out of it. A layering system only works as well as the poorest layer in the system (the weakest link in the chain, if you like). It doesn't matter if you are wearing the most breathable waterproof in the world, if you are wearing a cotton t-shirt underneath it, you will get cold and damp. Likewise, if you are wearing a non-breathable insulation piece underneath your shell, then that will limit the breathability of your clothing system – not the waterproof shell.
Your baselayer needs to wick moisture away from your skin, and your mid-layers need to provide insulation but allow moisture to pass out easily. Fleece is great at doing this in most environments, and for colder conditions, breathable insulation (like the Katabatic) works really well.
Wear the appropriate amount of clothing for your activity level. Start off cool (especially if you are going to be walking uphill) as you will soon warm up once you start moving. Add layers when you stop, rather than having to stop to take off layers when you are moving. Adding a waterproof layer will make you feel warmer, as it cuts out the effects of the wind. So when you put your shell on, you might want to consider removing a layer underneath to compensate. If you are wearing too much, you will sweat more and that means your clothing system must work harder to get rid of this moisture build up to stop you from feeling damp inside your shell. Insulation layers for static use i.e. down jackets, traditional synthetic insulation, are great if it is extremely cold or you are moving slowly, but often if you layer a waterproof shell over the top you will wind up overheating and accumulating moisture inside your shell. Keep those items for use when you are static, or if it's cold and dry use them as your outer layer instead of your waterproof shell.
A few top tips:
You don't have to wear your waterproof if it's not raining (shocker!). Yes it works as a windproof layer, but sometimes this is overkill and you'd be better off and more comfortable not wearing it
Keep it clean! Your waterproof will work better if you keep it clean and re-proof it when necessary
If you are running in a light weight shell, try to adjust your rucksack so it doesn't bounce around, as this can cause excess abrasion on lightweight fabrics
If you carry your ice axe down the back of your rucksack (between the shoulder straps), be careful where the adze sits: most fabrics aren't ice axe proof!