In case you did not know this, there are really 2 main purposes for having and using a dedicated audio interface, rather than a low-end sound card or on-board sound chip.
1. Inputs and outputs, along with microphone pre-amps and quality analog/digital converters. There are lots of different levels of quality and number of inputs and outputs, as well as with the converters. Many audio interfaces also have midi ports, as well, and most allow multiple outputs, such as to different sets of speakers.
2. The big thing about having a dedicated hardware audio interface is that the drivers (usually ASIO, but not always), take the massive load of analog/digital conversion off of the CPU and instead the audio interface has hardware circuitry that does all of that work.
Without a dedicated audio interface handling all of the work involved with analog/digital conversion, that work would all fall on your CPU, and this will make it VERY difficult for your computer to keep up with processing all of that data without sometimes dropping the ball. When this occurs, you get the crackles/pops/dropouts that you are/were experiencing.
When you are simply playing songs back through your computer speakers, your on-board sound capabilities are usually fine for the job, but when you are using a program like Sonar, you may EASILY overwhelm the native ability of your computer to keep up with it all.
I would recommend that you consider connecting both sets of speakers to the dedicated audio interface and using its routing capabilities to send sound output to whatever set of speakers you choose to use during that particular set of work in Sonar you are doing.
IF you choose to do this, I would recommend you start with the ASIO drivers and the following settings for both the interface and for Sonar, as a starting point for getting good quality sound output without cracks, pops, and dropouts:
For the audio interface: Sample Rate 44.1 or 48 k, ASIO Buffer Size of 128
For Sonar: Sample Rate of either 44.1 or 48 k (must match setting on interface), record bit-depth of 24, driver mode of ASIO.
I hope I have helped explain it, and I hope that you end up with something you can work with on a regular basis without having audio issues.
Bob Bone