Hi Subrat,
Let me answer your queries serially:
- Will this be washed away after upgrade as we are changing on standard configuration with access key ?
-[Answer]: Yes. If you are modifying in the standard configuration, then post upgrade the changes will be overwritten.
To avoid this, you can copy the application configuration, component configuration, and the screen(list/form) configuration. Make z components, and call them instead of the standard application.
- Will I be find deduction field in the structure?
-[Answer]: If the deductions are calculated and saved in the standard fields, then yes you should find it in the structure. However, if the deductions are calculate but not stored in any standard field, you can use nay of the unused fields in the structure to save the deductions.
- How about using enhancement spot option from addiontional function menu to add deduction field instead of going for adding column option.
-[Answer]: Enhancement would be the last resort for me. As we can achieve the required application look and feel using configurations itself.
Do let me know in case you have any further queries.... 
Best Regards,
Rohit Singhal