In addition to the panadapter, Figure 1 shows other connections that you probably have if you have connected your transceiver to a computer, and you are using, for example, a logging program. You don't need to change anything in these connections because of the addition of the panadapter. By creating the circuit shown in the figure, you will be able to simultaneously use the SDR receiver application and the logging application (in this example, SDRUno and Log4OM, respectively). In order for both applications to communicate with the transceiver at the same time, you need to use one more program, used to split the computer's serial port. Probably the most popular program of this type is the free Omni-Rig. In the settings of both applications, you then choose not the number of the actual serial port of your computer, but Omni-Rig. On the other hand, in the configuration of the Omni-Rig program itself, you set the actual port number to which the transceiver is connected.
If your transceiver does not have a USB interface, but an RS-232 interface, and the computer has only USB interfaces, you additionally need an RS-232 to USB converter. In the case of Yaesu transceivers, it is good to use the SCU-17 converter of the same company. Of course, the baud rate setting of the Omni-Rig must be the same as that of the transceiver, otherwise you won't get communication.
In the circuit shown in Figure 1, the frequency and mode settings are synchronized between the transceiver and both applications. For example, if we change the operating frequency by turning the knob on the transceiver, both applications will update their frequency settings. If we change the frequency by clicking on the waterfall chart in the SDR application, the transceiver will tune to the new frequency, and also the logging application will update its frequency value. Finally, if we click on the selected DX in the logging application's DX Cluster, both the transceiver and the SDR application will tune to the correct frequency and set the correct modulation type.
Nothing prevents you from running some other application, for example, for digital modes. You just need to make sure it is compatible with Omni-Rig. It, too, will synchronize with the transceiver and the existing applications.
The synchronization described above is possible only for transceivers equipped with CAT (Computer Aided Transceiver) system, i.e. those that have an interface for connecting a computer. If your transceiver does not have such an interface, it is still possible to use a panadapter based on an SDR receiver in an arrangement as in Figure 1, but you will then have to tune the transceiver and SDR independently.