Go to File>Record Setup>Sonar Setup:

In Select Sonar choose Klein 3000 / 3900

Select which Klein 3xxx sonar configuration from the options and hit OK

Launch the server by hitting the red record mode button in Isis:

The Klein 3000 server launches

If necessary change the default IP address then hit the ACTIVE button
The Isis main waterfall window will become active and the server will start incrementing the Triggers number.
You have successfully connected to the sonar.

Hit the STANDBY button and Enable MASTER sonar control to change ranges and pulse lengths, note that in this mode both the HF and LF channels are available.
NOTE: The server will automatically select the correct pulse length for any given range, you may override that selection and choose a shorter pulse length - however you may not select a longer pulse length. than the recommend one.

In this configuration Side Scan channels 1 and 2 are available and are used to log either HF or LF data, plus a single Sub Bottom Channel

Launch the server in the same way;

Note that you may only set the LF OR the HF pulse length - not both
To enable the sonar in Sub Bottom mode set the SubBottom check box, click Advanced Setup and Diagnostics to configure the data type:

Choose either 24 Bit or 16 bit data for the Sub Bottom Channel.

Note that in this mode Ch1 and Ch2 can log LF data OR HF data - not both.

Launch the server

Note that the title in the server is now Klein 3900 - (you must hit the ACTIVE button for the server to read the sonar type)