I had some confusion over this, too. I stopped getting the bonus, & then I only got it when I slept in some beds but not others. I thought it was a glitch but I finally just looked @ Active Effects & it's always there. However, the notice that flashes on the screen sometimes doesn't work, in some locations.
How the heck, though, do I get the lovers comfort? I can't get my husband to sleep @ same time. Is it because it's been a year in-game & I've never showered or brushed my teeth, lol? And why can't my character actually lay down on the bed? I couldn't do it in Oblivion & I can't in Skyrim either.
I haven't gotten married, yet, so I can't help you with your marital issues. Try bathing in a river?
But I do know that the well rested bonus for sleeping only applies if it is your bed (in a house or room you own) or a rented room at an inn. Sleeping in someone elses bed it does not apply. The Lovers Stone does the same as the Lovers Comfort bonus and you can't get the Comfort if you are a werewolf (vampire, too? not sure) or have the Stone active.
I try to sleep in my house for at least 8 hours before going to the market, giving a septum to a bum, then start selling stuff to up my Speech when trading. Skill raises faster and is boosted by the donation.