Archana,
For the purpose of project cost allocation you will have to use HR infotype 0315 - Time sheet defaults.
You will have to update the sender cost centre to which you would want to post the project cost. The employees would be able to enter activity / network relevant to the sender costcentre only.
The org.assignment costcentre is not very relevant to the project cost allocation. Ideally when any changes happen in the organisational assignment of an employee, the sender cost centre is also changed through activating dynamic actions. In other words, the master cost centre (In 0001 - organisational assignment) and sender cost centre is 0315 - timesheet defaults should be the same
Let me know if u have any questions.
Regards
Raj