Dear Space Case…
This is more an issue of clarity than of rules. To make your intention totally clear, use the old favorite ### to indicate all of your standard scene breaks. Where you want a special mid-scene line break, just leave the extra line space. I recommend not indenting the first sentence of the paragraph following that line space; I think this flush-left presentation will emphasize that the extra space is intentional. Lastly, just before the very first chapter in the manuscript, type this in italics surrounded by brackets: [In this manuscript, instances of extra line spacing between paragraphs are intentional to indicate mid-scene breaks.] That should make things plenty clear to an editor or agent reviewing the manuscript.