Ok, first off, if you're making a complete new overworld (I hope you do), first go to Layer 2 Event Editing and hold Page Up until it says Event 0x77 (or something) at the bottom of the Overworld Editor. Select everything on every map and delete them. do the same with Layer 1 Event Editing.
Now you don't have the original events happening.
In case you didn't read the Overworld tutorial before, then I'd suggest go and read it. You'll find it in the Documents section with the name Overworld Editing Tutorial (by Lordlazer).