I can only speak of how I use the upvote here on HN, but when I upvote something, It's not usually to express that I agree with the comment I'm upvoting. What I'm actually saying is "I think this comment is worth reading" -- it may make an interesting point, explain something in a clear way, etc., any of which can be true even if I disagree with an assertion the commenter is making.
If I feel the need to express agreement (or disagreement), I am much more likely to do that through my own comment in reply.
"So, lately, I've been trying to explicitly vote up comments which have replies, especially ones which have several replies, but aren't voted as highly as their children or peers."
I think it's proper to upvote the parent comment if you upvote a child comment. After all, you wanted the child comment to be better seen.
If I feel the need to express agreement (or disagreement), I am much more likely to do that through my own comment in reply.