How many serial inputs do you need. The Mega has 4 in hardware, one for the console and three for whatever. From the description the IDE has found more than one library. Search for them from the console. In windy dos enter from c:"dir SoftwareSerial.h" /s enter in Linux from the Terminal enter: find -n "SoftwareSerial.h" enter, Linux is case sensitive, dos is not. You should also be able to find it in the error output from the IDE.
Multiple libraries is not necessarily a problem. As far as I know, the ouput should tell you which one is used and which ones are ignored.
Your error might be caused by the "multiple libraries" if it picks the wrong library but often the error is totally unrelated.
When an error occurs, you should see a button "copy error messages" at the right hand side in the orange bar. Click it and post it here using code tags.