Open the software, go to the "File" or "Setup" menu, and select the matching COM port.
Vertex CE59 Programming Software: Essential Guide and Download Information
Essentially, Ce59 replaces the need for manual, button-based programming (which is often limited or non-existent on commercial-grade radios). It provides a graphical interface to manage all the complex parameters of your Vertex radio.
The is a Windows-based radio programming and cloning utility designed to configure various professional two-way radio series. Software Purpose and Features
Disclaimer: This post is for educational and archival purposes. FCC licensing applies. Proprietary software notices belong to Motorola Solutions/Vertex Standard. Use at your own risk.