After sleeping on it, I realized my previous response wasn't very productive or helpful, although it is difficult to offer constructive suggestions based on such little information.

Some things which would help to know would be:
How many O/D pairs are you looking at?
Are you shipper, consignee, or both?
Are your facilities mostly on any particular railroad?
What type of commodity or car type would you be using?
Are the facilities already on rail (this can be inferred as 'yes') or is building required?

Again, if you keep in mind that most short lines don't set rates, try and look at the big picture from the railroad's (mainly the Class 1) perspective. If you can, you might even get their marketing person to help draw the overall big picture as a service plan. That Class 1 contact would then, in turn, work with the short lines. You could even go directly to the short line marketing group at the Class 1. They can help you negotiate both internally at the Class 1 and at the short lines.