AlterBrains

Is it possible to modify a share component files without changing the main site layout?

You can create separate layouts per site and configure them in component settings if component has such settings and its config is not shared.

Where do i start? I am fairly new with this great software and you did the settings for me(great support) btw. When ever i config the mobile site components it affects the main site as well.

You need to know usual Joomla MVC first.
Your sites uses same database tables, so for sure changes will affect all sites. Each site should have separate contents, in this case different layouts will be applied.
Otherwise you can't use different layouts, or create a single layout override and display different contents by checking current domain manually.