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The upgrades are automatic but, unfortunately, some of the upgrades aren't noticeable.
I maxed out all of my weapons just because I wanted all of them to be maxed out, but some of the maxed out weapons are weak.
The items that I use the most are the Rhino, Sniper Mine, Repulsar Field, Agents of Dread, Killer Bee Mine, Acid Detonator, and the Electro Rocket. The other weapons are kind of weak and worthless... :(