MBP Audio Input only works in Garageband?

I have multiple audio/music apps installed. Can't get samples through my line-in via anything but Garageband; which I don't really use a lot. I use a Presonus USB audio interface when I'm in the office but at home or on the road I usually just plug in through the line-in built-in input. I literally can't get any audio to work unless I have an active track being monitored in GB. It's got to either be something I've really messed up or something incredibly simple that I'm missing (anti-feedback?). Here's all I have installed that I know of:
Traktor
Maschine 2
Audacity
Garageband
Soundflower
PreSonus Studio One 2 (basic)
Have checked through system pref/midi settings/audio routing for each of these apps... any ideas?
Thanks

Good Afternoon djLDB,
The resource below explains how to set up an Aggregate Device in the AudioMidi Setup, which may be helpful in configuring your audio interface for sound input/output. Click on the link for complete details.
How to combine multiple audio interfaces by creating an aggregate device - Apple Support
http://support.apple.com/en-us/HT202000
To set the System Setting in Audio Midi Setup:
From the Finder, choose Utilities from the Go menu. Open the AudioMIDI Setup application.
Control-click or right-click on the device you want to use and choose "Use this device for sound output" or "Use this device for sound input":
Close the Audio Midi Setup.
Information about products not manufactured by Apple, or independent websites not controlled or tested by Apple, is provided without recommendation or endorsement. Apple assumes no responsibility with regard to the selection, performance, or use of third-party websites or products. Apple makes no representations regarding third-party website accuracy or reliability. Risks are inherent in the use of the Internet. Contact the vendor for additional information.
Last Modified: Nov 8, 2014
Cheers,
Judy

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