This site is not for solicitation of services or 'purchasing' development. Please do not post requesting side mods/plugins and so on. Your thread will be removed, and you will receive a warning.
[*]1. locate the worlds folder in the server folder
[*]2.Copy the "forcedchunks.dat" file and paste it in the folder of the world you wish to have pixelmon in
Source: viewtopic.php?f=85&t=12696
If that doesn't work, you could always just do a single player world and copy the world file from the minecraft saves folder, into your server file, and import it. That's what I do, especially since I try to make my own custom maps. But I also use world paint after creating the world just so I know the files for pokemon to spawn/etc are there. Then I basically build the world to my liking then use MCedit for minor details. A lot of work, but gets the job done.