You'll need to write a script to take the data you have from your own IP database and output the data to match the CSV data. You'll need to ensure you map your physical locations to a location as listed in the GeoLiteCity-Location.csv file - Feel free to add your own as required.
The output of your script should match:
"IP start range in INT notation", "IP end range in INT notation","Location ID from GeoLiteCity-Location.csv"
Finally, after you concat the original data and your data, you'll run the mmutil tool: csv2dat.py
mmutils does nothing about duplicate IPs. You need to make sure that your input data does not over lap either already existing IPs, or itself in anyway. IE: If you have Public IP space and you want to identify where those spaces exist, you need to remove the already existing data from maxmind.