1. Where is an antimatter cub?
2. Where is upgrades for two last weapons?

I don't remember where the antimatter cube is, but for your second question....

For the green disk shooty thing upgrade, go to the swamp and to the left. There's a portal about half way through the room, and inside a save machine, a silver door to your left, and a guy to the right. He says not to try going into the blue smoke because he feels something grab him when he touches it. If you can make it to the end, past all of the blue smoke, you get the upgrade for it; this means when you shoot the blade comes back to you and you can catch it. I'm not sure if there's a specific way to make it past the smoke, but I just ran through with 20 hp + A med kit and tried to jump where I could.

The upgrade for the energy gun is part of one of the side quests. Go to the hell desert, and through the door in the middle. Half way into the map there's a seperate exit, go through there and make your way to the right of this level and someone from the vultures is in a hut. He gives you a pick axe and tells you to get some adamantium from machine town, when you give him the adamantium, he gives you the upgrade ^^

It is actually advisable not to pass the blue smoke at first. You get an item later on which makes that much easier. Unfortunately, at least I found that its description doesn't make clear that it's used in that part.

So, here's a spoiler: The blue smoke is caused by ghosts!

the antimatter orb is in desert hell east

just enter in and folow it around until you reach the far top right of the map, you have to doubkle jump up to a small chest like the one that was near the priest