For a proper job on them, I use the method Lowa seemed to be recommending which is to rinse and scrub the boots in water to clean and dampen the leather. Then spray with waterproofing spray whilst they're still damp, and let that dry which supposedly draws that stuff into the leather. Then I use a brush to apply whatever wax I fancy using - Ledergris or some beeswax stuff I've had for years, ensuring the seams and joins catch extra wax and then use the hairdryer to melt it all in. Brush them up the next day to remove any excess.
I don't do this after every walk, just when when they've got really wet and I can see the wax has come off. For shorter walks or dry walks they get either nothing or a quick brush over with a bit of wax. I do think you can overwax them if you're not careful.
I heard one theory is to heat the boots first, with a hairdryer and then apply wax and let it cool, again to draw the wax into the leather. No idea if it works.