Once the card application is operational, you will want to stage it in some service. Depending on the context, the client might be sending APDUs to it
- from a local application (e.g. a phone app sending APDUs to the UICC)
- over NFC (e.g. a merchant point of sale sending APDUs to a Visa application within a card)
- over-the-air, in a secure channel (the "credit" command would typically require that the entity sending it is authenticated, otherwise anyone can top-up their wallet)
It really comes down to what you are trying to build. In most cases you will have to build some reader code, most likely using PC/SC to send APDUs. Then the beauty of Javacard is that it lets you define your business rules within the card, that is within a tightly secured environment. Just make sure you can trust your inputs.