Travel advance deduction from payroll

Hi

Can you please tell me if the Travel Advance (Buisiness Travel) which is recoverable from employee deducted from his payroll impacts the TDS.

Is it a good practice to deduct it from Payroll or should we ask Employee to issue a cheque in companies name to clear the advance.

e.g. MR Employee takes Travel Advance of INR 100,000 for oversease business travel, he spends INR 40,000 and balance INR 60,000 is recoverable from him. Should we deduct this from his current months payroll or should we ask him to issue a chq of 60,000 in favor of company?

Thanks in advance

Girish