Vegas are the two scripts doing exactly the same thing? If so why create 2 seperate scripts its double the maintenance and the transaction response times for each iteration of the script is available to you.
You seem to want to use LR how it is supposed to be used but you are complicating it.
This is not a critisism, I'm trying to help you focus on teh fundamentals of LR (or any performance automation tool in general).
You should have kept different transaction names for the two scripts so that they can be easily identified by their names. If the transaction names are same in both then prefix it with some number. Lets say the first script goes with the series of 1_XYZ and the second script goes with 2_XYZ. As mark has already said if the two scripts have the same funtionality then you need not bother about the transaction response times of the two scripts. For future make sure that such confusion of transaction names do not happen.
In the Loadrunner analysis add the Web Page Breakdown Graph.This graph will give you reponse time of the transaction names of the two scripts.
I have recorded 2 scripts with URL www.zzzz.com by entering 2 different userdIDs and Passwords.I included Log In,Mail and Logout transaction as names .(#####In 2 scripts the transaction names are same#####)
In scenario i included these 2 scripts and ran the scenario with Vusers, ramp up time blah blah*.....here the problem is i want to analyze Log In,Mail and Log Out response times of 2 scripts differently.What i mean to say is
1. I need Login, Mail and Logout transaction response times of first script
2. Login, mail and Logout transaction response times of second script.
please don't suggest change the transaction names.