"Whenever I download a code I get a number of m format files after extracting that."
First step: extract the files to the MATLAB Search Path or the current directory.
"My question is how to use the m files?"
That depends on how their authors wrote them! Badly written submissions might include simple scripts, better submissions will include functions or classes that you can call after reading their help.
Some submissions might require compilation:
But if the files are basic .m files then you can just run them right away, following the instructions and help included with the files themselves.
Many FEX submission include demo files or examples in the online description. Most should include a help section in the .m files themselves, so you can use that to know how to use them. If they do not have a help section then give the FEX submission a one star rating!
"Should I use them separately as I get them or should I combine them and then run it to get the actual results?"
Most people want their FEX submissions to be as easy to use as possible, so I doubt that any authors would require their files to be "combined" or altered in any way whatsoever.