Hello Obee,
We understand that you want to maximize the usage of your Surface Book 2. By design, the batteries of Surface Book 2 charges and discharges at different rates. Whichever battery has less than 20% charge will be charged first. When both batteries are at 20%, the clipboard will charge to 85%, and then both batteries will charge to 100%.
For you to be able to maximize the use of Surface Book 2's clipboard, you can use it in studio mode, where-in the keyboard is still attached and folded under the screen. This means you can charge your Surface and use the USB ports, plus you'll have more battery time to draw, etc. To switch to Studio Mode, connect the screen and the keyboard so the back of the screen is facing the keys, and then close the keyboard. For more info, here's how to switch between modes on Surface Book or Surface Book 2.
As an addition to the number of great things you can do with your Surface Book 2, is that you can charge the clipboard and the base separately. If used as a tablet (detached), the Surface Connect port can be found at the side which attaches to the base and the base can still be charged without the clipboard through the usual Surface Connect port.
Let us know if you need more help by replying to this thread and we'll get back to you as soon as we can.
Thank you.