Hi Rakesh,
For your upgrade scenario there is no direct upgrade path. As per PAM you cannot directly upgrade from ECC 5.0 to ERP 6.0 EHP6.
Refer PAM link
Based on PAM and related information I could suggest following approach
1) Upgrade existing ECC 5.0 to ERP 6.0 on Windows 2003/ MSSQL 2005 ( System A)
2) Install a new system with ERP 6.0 on Windows 2008 R2/ MSSQL 2008 ( System B)
3) Perform homogenous system copy from system A to System B using export/import method.
4) Perform upgrade to ERP 6.0 EHP6 on System B post migration.
Hope this helps.
Regards,
Deepak Kori