The discolorazation is likely from water problems. Sweating and or dampness entering some where. This needs to be addressed first. Also check what type of floor you have down. This is a common problem on loose lay floors that only require glue or staples around the edges. What happens dampness gets under the floor and stains the vinyl especially loose lay floors. Sometimes the stain is caused from mold and on conventionally installed floors (completely glued down)water mixing with the glue. It manytimes dissappears when a conventional floor is installed. You will first need to remove the old floor or cover the existing floor with new subfloor boarding prior to a new floor. Be careful to check for soft spots in the subfloor a dead givaway that your subfloor will need repair also. work to seal up all areas where water can enter.