An application can only use one card at a time, as far as I know.
I have on-board and another internal soundcard. To choose which an appliction will use; right click on the speaker icon in the system tray and click on Adjust Audio Properties. On the Audio tab, select which sound card for playback, apply, then launch an application. You can then change which sound card for the next application.
This way it's possible to set up for Teamspeak/Ventrillo in your headphones, and LFS through your speakers, for example.
As they said above, reassign the axis when all controllers are plugged in.
Also, choose which device receives the force feedback - should be '1', '2'... buttons in the controller setup with multiple controllers.
I also get crackling since patch V... but I've also started using new headphones so could be that (I'd be dissapointed given the price of them).
It's only in the right ear, and appears linked to engine revs - not there when idling. I can't hear the cracking when using basey speakers. No screen stutter noticed
Given the above, it's quite likely the fault of hardware. I'd better investigate more!