You must pay Account Maintenance Charges (AMC), Depository Participant (DP) charges, and Smallcase charges by transferring funds from your registered NRE or NRO savings bank account to Zerodha through NEFT or IMPS. The funds will be updated in your account within 24 working hours. If they are not, create a ticket along with your bank statement showing the debit transaction.
You cannot use funds in your PIS account as the settlement for such charges does not come under the purview of the PIS regulations. You must ensure that there are no outstanding dues. The contract note does not display AMC and DP charges. You can view the due AMC and DP charges on your funds statement.