Ok, lets sort them out. You can give Virgil some items to wear, he collect himself items from the ground (especially wine and steel). So you could wear some more.
All the party NPCs (with the exception of Dog) will pick up items lying near them, on the ground. This becomes an annoyance when you purposefully want to drop stuff, which is why the developers added those bins. As you point out, they're cleaned regularly.
I'd suggest creating a few easy-to-access bases with chests in 'em, where you can leave items only to recover them as needed. There's one city fairly early on--the name escapes me--to the southeast of your starting point, where there are a pair of locked but unused guardposts. You can break them open and use the many chests they have for sorting and storing goods. Then, if you get the 5th level Conveynce spell, Teleportation (which is one of the best in the game, in my opinion), you can almost always spell your way back to this town. And since the guardposts are almost at the point where you enter, there's no tedious walking involved.
