Whenever I start Sonar up, any external audio cuts off. I have to go the control panel audio screen, select "recording devices", select "line-in", click "properties" and go to the "listen" tab. There is a checkbox labelled "Listen to this device". Sometimes it is now un-checked and I have to check it, other times it is still checked and I have to un-check and re-check it. Then the audio works. Anyone else had any problems like this, and is there a permanent solution?

What are you using as an audio interface?

Creative Labs X-Fi Titanium sound card

Without wishing to sound harsh, the permanent solution would be to invest in a decent soundcard/interface designed specifically for audio recording.
 
You can spend a little or a lot but the feature set will depend on what YOU want out of the system.
 
Will you be recording full bands? In which case you'd need one with at least 8 mic inputs.
If you're just recording yourself then a simpler unit with maybe 2 inputs & outputs will suffice
 
What's the spec of the computer you're using?