each time I download this file and try to unzip it the "current" folder and "A" file mix up as in=> current is a file, but works like a folder and A is a folder, and also works like a folder(both leading to the subsection of current).

I'm working in linux, but wether I try to install it prompt wise or just unzip it, it doesn't work, I can boot the game thought, but it gives me the message there are files missing and gives me to option to quit or either gives the files manually through the console.

Any ideas?(besides downloading it again, I've tried that a few times so far)

Sorry but i have absolutly no clue about what you did
What i do is to download the file (nexuiz-20.zip) open a shell and cd to the directory i want it to have.. for example cd ~/files/games then i unzip from there like unzip ~/files/downloads/nexuiz-20.zip and then i just cd into the new directory and start nexuiz. cd Nexuiz and ./nexuiz-linux.sh
All done from the shell..