Hi there,
Well, link cloaking can be done a few different ways, but you want to be careful in how you do it. Search engines see it as manipulating them, so sometimes you can get punished ... and of course, the rules are always changing.
You have to learn those rules ... so, reading like you're doing is good. Learn when to cloak and when not to even for the same affiliate link.
Some of us have cloaking tools we use to help us, but we don't use them every time.
Some affiliate networks like LinkConnector and Kowabunga (I think they still offer it) have naked link technology which is basically cloaked links right from the get-go ... but you have to contact your Affiliate Manager and ask them to hook you up to it.
This thread should probably be in the Newbie Forum too

... that's where you can ask all kinda of questions and get help.