I need to write a piece of code where i need to port databetween two sql databases hosted on different sql servers. I was wondering what was the easiest way of getting nhibernate to work on 2 connections?

I currently configure nhibernate connection through my web.config file, can i still do this using 2 connections?

This is conjecture, but I'd think you might try using two SessionFactory objects. I expect you'd have to set their connection strings programmatically, not from the web.config. See http://nhibernate.sourceforge.net/forum/viewtopic.php?t=1241 for that part.