I'm not a big fan of the stock Intel HSF either, lol. It's complete junk basically, and it's barely adequate if you never OC, but that's it. That and the pin design to hold it in is just stupid.
And like I said, I've never had a problem with my method of thermal paste application, but there are MANY different ways to do it, as you've seen. I'd say the way I do it is as trustworthy as any other.
Ideally, you want the same amount of intake and exhaust fans so that you're taking in and exhausting around the same volume of air, but if I had to err on one side or the other, I'd say another exhaust fan is probably a little better.