Manjula,
If you do a pipe stress analysis, it is always better to do the whole system analysis in one file. I don't like it either because it is a pain waiting for the whole model to regenerate everytime you change something.
You should not rely on your piping isometrics are basis on where to isolate stress analysis, always have your P&ID beside you.
My concept is that I only make another stress run for branches having a 1:25 ratio with section modulus of the main header line. Because, the effects of displacements/movements of the smaller line won't do much contribution to the main header line. But, keep in mind that you need to input all necessary data for the main-branch connections such as SIFs, allowables, etc...
Goodluck!