I thought this was possible in the old version, that dropping dirt with your hands did fill but I guess it now only changes terrain not adds to terrain. It is creative that has that feature of dirt dropping fills but that is infinite dirt source. But this is survival you have to keep the balance - if you dig one by one you should only be able to fill one by one using the same tool
Certainly a shovel could be the mechanic for distinguishing those changing and filling. And a wheelbarrow as a portable inventory would be a good way for doing bulk fills by doing inventory shuffling, but how would you indicate you want to just drop the inventory items on the ground vs. fill the terrain?
IN creative mode you can absolutely fill water holes this way. terrain not only blocks water it displaces water. Though it can be tricky if not using drop fill instead of area fill you tend to leave voids of water.
That may well be, I don't know, I play only survival mode, not creative. I'd just like a bit more terrain shaping there too. Filling a hole, and removing water, I would think, isn't anything special, you can do that in real life too with an actual shovel and a bucket, so why not in survival mode too?
Also, you don't dig one by one either: with the pickaxe, but even with the primitive stone axe, you remove quite a big portion of dirt or rock all at once - vacating a much larger area than just a single voxel. But currently you can only fill it back up block by block - I wouldn't think of that as balance.
Yeah, wheelbarrow is a good idea too, nice.
As for your question, I don't think you'd even need to distinguish that, just go by the contents: if there's ground material in it - rocks, dirt or sand - you will do terrain filling. If any regular items, then dropping them on the ground. And yes, this does mean that if you are transporting ground material with it, then you'll have to "dig" it again to pick it back up... but that's just how it is in real life too, isn't it? 