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... :( --- PC, PSP, PS3, Xbox 360, Wii
^ Are you kidding? Optical Maser Array is ridiculously powerful without being RYNO strong. They have some good mods for it also.
Armoogeddon is also pretty broken and unlike the others, when you begin a New Game + you won't find its effectiveness diminished due to the buff given to enemies. --- An infant sea turtle is actually capable of killing an adult African bull elephant. It does, however, require a substantial amount of surprise.