I play on xbox one.
I wanted people to know this because I searched online quite a bit and half of the people said one thing and the other half said another about this. It might be platform specific (PS4, xbox, PC) but on xbox, if you don't drop an item and scrap it manually, you will lose any extra items that the junk could have been scrapped for if you only use part of it during a mod.
For example:
A roll of duct tape will scrap into 1 adhesive and 1 cloth. Now lets say you want to mod a pistol and the mod takes 1 adhesive along with other stuff. You could just leave the duct tape in your inventory and make the mod, but you will lose that 1 cloth that you could have got if you had dropped the duct tape on the ground and opened the workshop and scrapped the item.
I have tested this extensively on xb1 and can verify you definitely LOSE the extra items.
Kinda wish I had known this at first... I think the game should give you the spare items; the 1 cloth from the duct tape in my example. It is very time consuming to drop everything and continually scrap so many items because I don't want to lose so much useful scrap. Especially on console. With keyboard and mouse it might be easier, but I bet its still a pain in the rear.