Raja,
I assume you have the IVIVC toolkit, I would recommend that at this time you use WNL 5.3 since the Phoenix implementation of IVIVC will be in 6.2 which will be the end of the year.
Data wise there are examples in the documentation; Example files are given of possible formats in the WinNonlin\Examples folder. e.g. ivivc_diss.pwo, ivivc_vivo.pwo and ivivc_test.pwo.
Chapter 8 of the Examples guide, (at least in the 5.2.1 guide), is dedicated to stepping through this project. Then you could set up your files in a similar format, or at least you will understand some of the mapping options available to you. The key thing is to keep formulation names consistent between vitro and vivo data to ensure the program can match up the profiles.
If you need to follow up on this topic; then you'll need to ask some more specific questions about exactly what is causing you trouble; or attend one of our training courses. If you don't see the one you're interested in listed publically you can request either onsite training at your company or institution's site; or you can request to be added to a wait list. Once we have several people interested in a region on a topic then we endeavour to schedule a public course on that module.
Also have you tried watching the recorded webinars e.g.
IVIVC Applications and Case Studies
IVIVC Toolkit for WinNonlin: Product Introduction & Demonstration