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.
If you edit the Mod Options/P menu settings, those will only apply to single player as you noticed. You'll want to edit the "pixelmon.hocon" file in the server's "config" folder, instead. You can use your host's file manager for that, or use an FTP client like WinSCP to open them locally in something like Notepad++.
After saving your changes, use "/pokereload" or restart the server to have them apply. Some settings may only apply after a restart. Make sure you keep the config's formatting intact, as any syntax errors will cause the mod to revert to defaults (with a big log error) on restart.