Yeah, as Irock said, just rename your icon set as "Iconset". If you want to replace any of the existing RTP files in the System Folder, just rename a file the name of an existing file. For instance, if you want a new title screen image, then make your title screen and name it "Title" and put it in the Systems folder. That'll remove the RTP title and replace it with your own. As you've learned, same goes for the Iconset. This also goes the same for all the tile sets. You can only have 4 different tilesets. B, C, D, and E. TileA is broken into several different pages of autotiles. TileA1, TileA2, TileA3 and TileA4. Just make sure you know what you're replacing.
As for what Irock was saying about only having 1 iconset, he's correct. You have to put all the icons you have into one iconset. The iconsets can only be 384px wide but can be as tall as you want. Each icon is 24px by 24px. You can do the math.