Let me try to help here.
-Copy the .3DS romfile into the ctrtool folder using Windows Explorer.
-While on Windows Explorer, go back/up one directory from the ctrtool one (if you are in it).
-Press and hold Shift key on your keyboard while "right clicking" with your mouse while pointing the ctrtool folder.
-On the menu that appears, select "open command window here", or something like that.
-A CMD window will open in the ctrtool folder (if you followed the instructions correctly), and you will be able to put in the commands needed to make the conversion.
Can't be any easier than this.
-Copy the .3DS romfile into the ctrtool folder using Windows Explorer.
-While on Windows Explorer, go back/up one directory from the ctrtool one (if you are in it).
-Press and hold Shift key on your keyboard while "right clicking" with your mouse while pointing the ctrtool folder.
-On the menu that appears, select "open command window here", or something like that.
-A CMD window will open in the ctrtool folder (if you followed the instructions correctly), and you will be able to put in the commands needed to make the conversion.
Can't be any easier than this.