the reason for capping them is just leak protection, I'd use the, just in case there is an accident
never heard of zerex, I've heard of Xerox though 
The best place to put a probe is under your cpu, so it is touching the bottom. Joe did an article on this a while back, so you can use that.
And I'm not entirely sure what you mean by your last comment, what is your problem here exactly?
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