The Minecarts with Hoppers are very confusing and after looking into Minecraft wiki page I couldn't find an answer on how I should use the hoppers.
What are some of the uses for Minecarts with Hoppers and how should I use them?
Hopper minecarts are useful for advanced redstone machines and automation, however, in many instances, you'll find that using a storage minecart to be more useful. For simple transport, storage minecarts hold more, and are automatically emptied the same way: with a hopper beneath the track.
The one main advantage with using a hopper minecart instead of a storage minecart would be to automate some farms, such as melon or pumpkin farms. Hopper minecarts can pick up item entities on and around the track, allowing you to break the melon or pumpkin with a piston, and have the minecart pick everything up instead of making you walk through the farm, although in my brief testing, the naive design isn't great.
Like many other things in Minecraft, you're really only limited by your imagination as to what you can build.