You don't really use scratchpads as your current palette, they are a separate additional system that achieves the same result. They act like mini-tilemaps. You can make as many as you want, name them, make them different sizes, and they are all saved automatically. They allow you to separate your one big palette out into lots of mini-palettes containing whatever custom arrangements of tiles you want.
The same controls work in the scratchpad as on the main tilemap - so you know how you can use the Alt key (the eyedropper) to 'pick up' tiles from your tilemap and paint with them? Scratchpads work the same way - hold Alt and click or drag-select on the scratchpad to select tiles from one, then paint with those tiles. Or select the whole scratchpad with 'Select All' or the Enter key.
They work well with keyboard controls as well:
1. press Tab
2. type the first few letters of the scratchpad name (or use the up/down arrow keys)
3. press Enter
4. now your brush contains all of the tiles from that scratchpad ready to be painted into your main tilemap