How to make my datasource multi-instance

When you create a new Datasource you will have the option to check a "multi-instance" box. You can't easily change it after creating the DataSource as it's greyed out in the UI. You can either export and edit the XML directly or best to just create a new DataSource with that option enabled and copy over the settings/script. Once you enable that option you can optionally choose to use an Active Discovery script or not. If you disable this option, then you can use "add monitoring instance" on the device (resource tab) to manually add instances. If you enable Active Discovery, you can automate the addition of customer instances, assuming you have a source list you can query. Note that using BatchScript is generally more efficient than using plain Script when it can be used.

Side note. It sounds like you might be an MSP? Keep in mind that DataSources will always run on the collector systems. So you don't want to collect data for one customer from another customer's collector. Best to do something like that from a collector you directly own. Unless by "customer" you mean your customer's customer.