When looking through your inventory, stolen items or stacks that contain stolen items will, when selected, display the word "stolen" in red. While this is slightly tedious, it's no more tedious than any of the other normal inventory management tasks I undertake whenever I return to my home or, early in the game, the container I use for temporary storage. (Personally, I like the dresser between the male & female wings of the the Companions' barracks.) Let's face it, your carrying capacity is a valuable commodity.
Stashing away your stolen goods is an important habit for light fingered Dovakin. Privacy is also important here, as recovering a stolen item will look like another act of theft, so be careful here. This is where owning a Home and the containers therein is nice, as your housecarl or any members of your own household will generally not report you to the town guard.
To separate stolen items from a stack, you can drop the stack on the ground/floor and the items will hit the floor in stacks of stolen or un-stolen items. Pick up the stolen items, stash/fence, then pick up the items that are actually yours. Again, this is a task best done in private/at home.