How and if to advise editor about suitable referees for my paper
This certainly sounds like it could be communicated through a cover letter. This does not guarantee that your comments are actually being read by the associate editor, though - at least in my field, cover letters are uncommon enough for journal papers that I typically don't even check if there is one if I get a paper to handle. However, it is unclear to me what practical other ways you have to communicate with a handling editor where you don't know yet who it will be.

That said, you never have a guarantee that the editor will take your input on reviewers into account. Personally, I tend to be fairly sceptical about "suggested reviewers" or anything that approaches this - maybe I am too suspicious, but whenever authors suggest a reviewer, especially when not explicitly asked to do so, I immediately assume that this reviewer will be in some way positively biased, even if no conflict is obvious from the outside. 

So my summary is - sure, (briefly) explain your reasoning in the cover letter, but don't get your hopes up too much that this will change substantially how your manuscript will be handled.