Sims will not use a desk to do their homework unless it happens to be The One Desk.
I'm talking about when using Dizzy2's Homework in Bedroom hack.  They will seek a desk in their bedroom first and put their homework there.  If there is not a desk or table in their bedroom, they will look outside their bedroom.  I use the sleep clock, so my sim kids pretty much know which bed is theirs.  I think the problem is just the design of this house.