No. The program doesn't work for online music or for music played on Youtube. You need to load the audio files in TwelveKeys application in order to make modifications to them. It isn't advised to use recorded files or files that you downloaded directly from Youtube because they have a low quality.
On the official website of the product, there is no information regarding the use of a guitar as an input device. To find out more about this, you should contact the developer using the site mentioned.