Returning player,
EVE Pilot requires its specific UI settings, but I want to be able to launch with my own for when I play manually.
If I remember correctly, we just made different copies of EVE to solve this before.
But now I think settings are shared? How do I go about setting up the two and switch between them?

thanks in advance

There are no good way to separate bot and player settings. You can:

1) create new window user and login under this user when you bot. You may also try to start bot from different user without relogin. With shift pressed right click to evepilot.exe ->run as different user. In compatibility tab of evepilot.exe, just in case, tick run as admin. I did not check how the method without relogin will work.

2) Do all setings you need in game. Restart evelauncher. Open evelauncher profiles and copy your default profile to profile with different name, e.g. MyProfile. When you start bot, bot will replace profile with name "Default" but will not touch anything in "MyProfile". When you play manually again, open profiles. Create MyProfile again (no need to copy settings from default this time) and switch to it.