Welcome @Dredzior!
~~At the moment (June 2019), the way to apply settings to a bot is to add them into the bot program code, just like the operation logic.
I will soon add a simpler way to apply settings, without the need to modify the bot program code. Will post an update once this is done, at least at https://forum.botlab.org/t/botengine-devlog/2183~~
Update 2019-06-18 (from BotLab Devlog - #18 by Viir):
I added new functionality to the botengine console to address this problem: You can now use the new --bot-configuration parameter to apply the settings to your bot when you start it.
I updated the guide to illustrate how this new feature is used, including an example command line: bots/guide/how-to-use-eve-online-bots.md at cac1a1f9443786326ee03aaa59bac309805e696e · Viir/bots · GitHub