Most of my presets sound pretty good with the coil tap. OP, you have several options if you want to use a preset with both pickup settings. One simple option would be to put an EQ block in your chain with a few db boost. You could also set the EQ to tweak the sound of the single coils if needed.
You could have different input trim settings as well as Drive and Master settings that could be engaged by scene. For example, let's say you want to bump the input trim from 1.00 to 1.5 when you coil tap. Attach the input trim to the Scene 1 controller. Under the scene ! controller there will be level settings for each of the 8 possible scenes so for scene 1 set the knob to 50%, which is noon, which is 1.00 on the input trim. For scene 2, set it 75%, which is 1.5 for the input trim. Now when you go from scene 1 with hum buckers to scene 2 with single coils, it'll up the input trim.
You can make it more complicated by using the 2nd Scene controller to adjust the drive or any other parameter as well.
Lastly, you can attach the the boost switch in the amp to a button on your floor controller.
There's probably several other things to do, but those are the most common approaches.