Base on some forum postings i have found, i went ahead and create a Flat Rate Late fee, which will then be run weekly with the Automated Work flow.
Please find my script i'm using:

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//create a variable to get invoice total and add a $5 LateFee
latefee = 5;
orgID = organization.get("organization_id").toString();
invoiceID = invoice.get("invoice_id").toLong();

//display the value stored in the latefee variable
info latefee;

//add late fee and adjustment and store the total amount in the variable 'adjustment' 
adjustment = invoice.get("adjustment").toDecimal() + latefee;
jsonMap = Map();
jsonMap.put("adjustment",adjustment);
jsonMap.put("reason","Automate: Weekly Late fee");

// To update the current record
result = zoho.invoice.update("invoices",orgID,invoiceID,jsonMap);
info result.toMap().get("message");

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Taking note that this script is updating the "Adjusment Field" and adds the late fee to what ever is in that field (I do use that field also for a Late fee for Late payment of 1st deposit).
Now when sending out my reminder email, i want to use that the "Adjustment" variable to show the client, his/her outstanding amount in latefees, however: if they did had a LatePayment for their deposit, this will be reflected also, so to avoid that this is what i did.

I created a Custom Field in the Invoice tempalte, name "LateFeeBalance"

My objective is that when i run the above script, it also takes the LATE Fee and add it to the LateFeeBalance custom field, so that i can then use this as a placeholder in my reminder email,

see example below

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