Paying directly to EMGS is always less hectic and time consuming. Now if you have already chosen it through the institute, you are required to send the fee (that appeared on EMGS application) to your institute. Just ask the institute their banking details, transfer the payment, and the institute will make payment to EMGS on your behalf. So make hard copies of all the documents you have submitted to EMGS, along with the copy of VAL application and proof of payment to institute, send to them to your institute.
Paying directly to EMGS is always less hectic and time consuming. Now if you have already chosen it through the institute, you are required to send the fee (that appeared on EMGS application) to your institute. Just ask the institute their banking details, transfer the payment, and the institute will make payment to EMGS on your behalf. So make hard copies of all the documents you have submitted to EMGS, along with the copy of VAL application and proof of payment to institute, send to them to your institute.