is it a cloud based system?
if it's a cloud system then :
what we do when we have a similar project :
1- once web service
2- On Admin Portal (Asp.net or B4J)
then the below is for each customer :
1- Each customer has his own database on the server (meaning if the customer name is erel then the database will named erel)
2- Each customer will have his own app - different package name of the app and different logo + name (meaning if the app is for delivery then each customer will have his own folder and that folder contains the project : WHY ?
because some customers will require some customization in the system and you can't make the customization effect all the other customers)
Hope that answered your question and if you have any question regarding the above just send me a PM and i will be more than happy to help through the process