Yeah very basic title, sorry but wasn't sure what to title this. Anyway, the issue I'm having I'm pretty sure is just a configuration issue but when I have myself or anyone enter or exit a nether portal it seems to only lead to the same point. To get a bit more specific I can make a nether portal anywhere in my main world but when I enter it it always takes me to the same place in the nether, And vice versa. Like I said this is probably a configuration issue but I've looked through the wiki and have yet to find anything. So if anyone has any fixes or advice it would be greatly appreciated.

This sounds like a very common issue that is due to the portals in your overworld being too close (within 1024 blocks of each other). If so, this wouldn't have anything to do with Multiverse-NetherPortals or your configuration of it. See http://www.minecraftwiki.net/wiki/Nether_Portal#Linkage_between_Overworld_and_Nether

Yep that's what it turned out to be, teleported to coords much further away and tried and it seemed to work as intended. Thanks.