My Downloads stack is at the top of my home directory (i.e. users/name/Downloads). You seem to be correct on your query though- and it's not that dumb! There is at least the 'show in Finder' option on the stack itself, which I find easiest.
Ah yes! I missed the 'Show in Finder'! Thats just fine.
I have a Mail download in both places - one timed at 08.53 and one 09.14. I think I dragged it to the desk-top once & downloaded it once but I cant really remember - I must experiment to see what has happened!