If you just need to disable some layers you can do this in yaml file (https://github.com/openmaptiles/openmaptiles/blob/master/openmaptiles.yaml).
If you need to change a content of a layer - definitions are in layers directory (https://github.com/openmaptiles/openmaptiles/tree/master/layers), if you'll get familiar with files inside each directory you should find out what's going on there. Also I advise you to get familiar with osm tagging. Changing layer's definitions is not a simple task for a beginner and AFAIK there is no WYSIWYG or even GUI tool for this. Every single change here could significantly increase time of preparing data, tile's sizes and decrease performance... Also next thing is that I didn't found any detailed-enough documentation so I had to do everything by myself analyzing the individual files and the relations between them. I regret that I didn't made one after all, but the project has been abandoned - and now, it was some time ago and I forgot most of it...