Question about slicing

I own a Makerbot Replicator 2, so I have to use an .X3G file format when feeding into my printer. I am wanting to slice an .STL file using Slic3r, which creates a gCode file. If I feed that gCode file into Makerware, does that in turn slice it again when createing the .X3G file, therefore making my initial slice in Slic3r obsolete? Kind of confused how this tool path works using an outside slicer and my Replicator.

Thanks

You might be better off loading up Sailfish which is tailored for the Replicators and other MakerBot machines?

I have been seeing a little about Sailfish, is that firmware for the actual machine or another slicing engine?