Comment on exactly what you mean. Today a comment attaches to a whole paragraph, so pointing at one sentence marks everything around it. Soon you'll select the words you're talking about and comment on those, the way you would in any modern editor.
Counterparties will actually find it. The most common thing we hear is that external reviewers don't notice comments exist and send their feedback by email instead — so the discussion leaves the contract, and the audit trail with it. Commenting is being made obvious for everyone who opens a document, including people who can only read it.
Know why something was rejected. Right now a proposal is accepted or rejected and that's the end of it. You'll be able to reply before deciding, so the other side gets a reason rather than a silent no.
See what happened in the activity log. Today it records that someone accepted or declined a proposal — but not which one. The log will show the change, the comment behind it, and who decided what.