There are two ways to achive this, but there are two slightly different circumstances you need to consider.
1. Uploading the application to a new module from Digi:
For this you need to use FTP.
Use a windows command prompt to FTP to the unit you need to program. Once you are connected and logged in simply "PUT" the image.bin file that is crerated in the debug folder of your project.
Once the program is uploaded exit the FTP session and the module should reboot with your application in it.
BEWARE!!! if things go wrong here or the application is incorrect it is possible to leave yourself in a position where the module does not boot and then it is very difficult if not impossible to access it.
2. Reprogramming a module that has your own application in it.
Once you have an application you may want to update it in the future. To do this you must include the reprogramming capability in your application.
I am assuming that you are using Digi ESP and NetOS. I have found the best way to do this is to start developing your new application with the New NetOS Wizard. When you do this be sure to include the Webserver, and the FTP Server. If you include these the wizard will generate a project that include the FTP functionality described above, but it also includes an option in the Web Server interface that allows you to "Upload Firmware". Select this link in the Web interface and select the "image.bin" file, and it will be uploaded and the unit programmed.
WARNING: as above test the functionality carefully with the JTAG version before you try to do this with standard units to avoid trashing modules.