@Dopedangel,
If I might ask, in what way are you finding that cover.jpeg 'doesn't work'. I have about 40 epubs on my Android phone. Most, if not all, of them have a cover.jpeg file for the cover as I have been routinely using 'Modify Epub' to put them there using the 'replace cover' option.
Whilst CoolReader is not my No.1 choice for reader app, I do occasionally use it. I've just checked again, all my epubs are correctly displaying cover thumbnails.
I have a vague memory that CoolReader didn't always show cover thumbnails if the opf file didn't contain a metadata item similar to
Code:
<meta name="cover" content="cover"/>
Using 'Modify Epub' or the new calibre 'Polish - update cover' should automatically fix that, though.