This is an old thread, but I had a similar problem with my TT in that I couldn't seem to figure out how to overwrite the four factory presets, and none of the prior solutions worked for me. I just figured out how to do it.
1. Select the desired tone, click the "Cloud" icon along the top of the app, click the "Save" icon in the top right corner, then select "Save to My Tones".
2. In "My Tones" select the desired tone to be stored in the presets.
3. In the top right corner will be three vertical squares. Click on those, then select "Save to Hardware". This will display the contents of every bank.
4. Select the preset that you wish to overwrite, then confirm the update.