Salary and fees both are deductible expenses from Income tax point of view, as it's solely done for business. Yes but when u pay fees, and the party is changing service tax, if input tax credit is available for such services in your case, then u can avail such input tax credit. And even when u pay salary, u may need to deduct TDS.
I agree with Ankita gandhi, in both payments you have to deduct TDS if applicable, but as simply you want to see this matter from point of view of liquidity you should opt for salary as it includes salary amount (-) TDS if any. and fees includes fees + service tax (-) TDS. you compare the amount you come to know that salary is better option as outflow of money is lesser. You can use time value of money concept also.