As far as the kernel goes, I simply renamed my existing kernel file "scrypt130511.cl" to "scrypt130511.cl.backup", and then copied the modified "scrypt130511.cl" file in to the same location as the backup. I didn't specify anything in my arguments, the miner just picks it up. Incidentally, how can you tell which .cl file the miner is using?

CGWatcher just gives you a nicer way to look at your stats, but I prefer to just look in the miner window since it's gives you immediate stats on what it's doing right that second. I primarily use CGWatcher because it can reboot the miner or even your computer if things crash. But it has a ton of other cool features like e-mail updates (which I just discovered yesterday, pretty cool). I notice that my hash rates jump up and down a lot in the first 15 or so minutes that the miner starts, so any time you make a change to your settings give it at least that long before determining if what you've changed helps or not. After it's been running for several hours the average rates should hardly change much at all. If it continues to jump around for a long time it may mean you're getting errors or lots of rejects (so I've heard).

That's as much as I know right now. Feel like I'll never be an expert at this though since there seem to be no end to the variables that can influence performance. Wish I were an engineer, alas I'm just a lay person trying to make a buck.