I presume the following circumstances in your case:
1. Your company provides 2-wheelers and 4-wheelers to your staff for commuting on company matters (no separate drivers).
2. The company tries to avoid paying the petrol or diesel bills as reimbursement to those staff for these trips undertaken by them for company affairs.
3. Repair/replacement costs will be met by the company.
If so, my opinions/suggestions are:
1. Fix mileage per vehicle/per liter of petrol or diesel after considering individually the model/year, condition of the vehicle, city road/traffic conditions (you may obtain the opinion of a popular auto workshop/service garage/shop for your records). Keep this as a thumb rule for paying the mileage allowance for company trips.
2. All the staff who are provided these vehicles should maintain a register on a daily basis recording trip-wise information - such as - from office to customer's place - kilometers traveled onward say 10 kms, return 10 kms. Likewise, each and every trip should be recorded under various columns. Total up the kilometers traveled either every weekend, say Monday to Friday, or from date 1st to 15th or 1st to 31st. Thus, the total mileage traveled say 100 kms.
And if a two-wheeler, it gives 35 kms./per liter of petrol. So 100 kms. divided by 35 kms. = 2.86 liters. Then 2.86 x Rs.65/per liter of petrol = Rs.185.90, say Rs.186/- pay individually through you.
3. By this method, you will also help to avoid income tax problems (if you pay conveyance allowance, it will be taxable as per IT formula).
Alternatively, if you don't follow these procedures, simplify by just obtaining a claim from them certified by their HOD saying so and so has covered ...kms. during the month for official duties and at a mileage allowance @ Rs.5/- per km pay him the money through individual you (rate per km has to be decided by you).
Paying through Salary bill will attract IT. But if you want to jack up the CTC then calculate a monthly allowance based on the projected kms. one has to travel in a month and fix up a monthly allowance, pay through a salary bill. But repairs & maintenance, running costs exceeding the expected kms. to cover have to be answered.
Consider various options and adopt what is best suited to you.
Regards, Kumar, Bg.