Thanks for keeping us posted with your questions, epad03. 

You can enter the amount that will come in from your bank feeds, as you mentioned the partial payment of $3,000. This way it'll match to the amount posted in the bank downloaded deposits. You can check these screenshots below for your reference on how it'll look like. 

You can follow the same steps every time you customer pays you with a specific amount. You can also check out this article for more details on how to manage bank downloaded transactions before you reconcile an account. 

The Community is always open to help you. Just leave a reply below and my colleagues and I will surely assist you. You keep safe always!