>>If I make duplicate of the same file , exclude original startup file from build then its working fine.Is this right way?
yes, but do this in the project, not in the SDK respository.
If you modify the startup code in the SDK (from where the projects get created/copied), then of course this will affect all projects you will generate from that SDK. I recommend that you add the SDKs as ZIP files to the IDE, then the files will be copied and you keep the original SDK files intact.

I hope this helps,
Erich