Use this link
http://www.mangago.me/genre/Yaoi/
Then where it says 'sort by', click either views or popularity or whatever you want.
Sorry you can cancel the Yaoi out if you want there. It's my go to so I selected it without thinking haha.
How to search..
1 On the Top area, Choose Yaoi, Shoujo, etc.,
2 Sort by : Popularity
From that page, you can do more advance search.
It's not stupid question at all.. Most users don't know how to search because they get use to ask whatever at Question Section. (▰˘◡˘▰)
This is probably a stupid question, but is there a way to search based on the manga rating? Highest to lowest rated?