If you have alsamixer installed use the command amixer to automatically switch the PCM capture source to the Mic.
For me this was: amixer -c 1 sset 'PCM Capture Source' 'External Mic'
Run this at startup by saving as an executable script and adding to Startup applications or by using /etc/init/. -c 1 selects card 1 (the Soundblaster G5 in my case). You can run amixer -c 1 get 'PCM Capture Source' to get the other options like 'What U Hear'. Plus you can also set your appropriate volume/gain etc using alsamixer to save those.