Hi Sanjeev
you can update the cost center Via PPOME for Individual employee's, but for Mass upload cost Center we need to use PP02 in LSMW. Check ur LSMW once again as Mithun suggested as it will automatically update the IT0001 at position level.
Note: Cost Center's can be updated at Org unit level,Job level, Position level, if u use PP02 then it updates all. Try & let us know the possible outcomes.
Hope this Info will be helpful
Cheers
Pradyp