--remove ?
Ok, so normally I would input the hash type with -m 10 and then follow it with --remove to have it remove all found hashes in my txt file and leave what isnt. Then I would output the found hashes by cudahashcat64 -m 0 --username --show --outfile-format 2 new.txt -o found.txt

It use to output the selected file with no issues, now for some reason it outputs nothing, what am I doing wrong?
You can't use --show after using --remove, as --show will have nothing to show since you used --remove to remove the cracked hashes from the list. There will be no matching entries in the hash list, they will have been removed.
Ok so I have a file with mixed MD5, and MD5 password.salt, I want to run the md5 Salt obviously first because if not running just md5 will output weird characters in the found.txt. I only want to leave what it hasnt found in the text file, but im assuming there is no way to do that.
Any ideas?
It is all very well explained in the FAQ: --show

To sum it up: --show needs to be run on the original (not modified) hash list, it must be run after the cracking was already finished and --left is the "opposite" of --show
Great, so with my MD5 pass salt passes I run it through hashcat, and whatever it finds I output to found.txt then I output a --left txt file to show me whats left. The remainder that I didnt find with MD5 Pass, salt I run with just MD5. Even though the FAQ didnt help, what you said did. Thanks!

Also, dont forget when you use --left you have to change the outfile format to 1 because you have no cracked passwords so it cant be variable 2!

Another question, if you do -m 0 when you are outputting the --left, Will only output the MD5 it found? I noticed I get two different results when I do -m 0 and -m 10 , My thinking is that it is outputting what is LEFT of MD5 and MD5(pass,salt)