1. The Fatal error you see, should be this one:
https://toolset.com/forums/topic/activating-layouts-plugin-breaks-frontend-category-display-with-php-fatal-error/
As far I know, this should be solved with the latest Update.
To confirm this, I asked the Developers for a statement, but could you confirm to me, if with the latest update the error is solved?
2. Can I disconnect layouts from the standard Woo function and use it only in the custom searches I've created?
I am not 100% what you mean by the "Woo function", but I assume, you ask if it's possible to use Layouts on certain content of your Website, but not on others, like in WooCommerce Content.
This is partially possible.
For WooCommerce, you use the WooCommerce Views Plugin and under it's settings (Toolset > WooCommerce Views) you can choose what template to use for what kind of content.
But this is relatively limited, so it does not allow you to filter single content of WooCommerce.
The idea is that when you use Layouts, you generally want to use it all over your Site.
Now, if #1 is solved, I usually should ask for a new ticket so to handle new issues.
It's a bit overkill to ask for that in this very case here, so if your first issue is solved we can, if you wish, proceed with issue #2 as well here, or, perfect would be in a new thread.
I would as first need to know, if you ulitamtely would like to use Layouts everywhere, and then, where it does not work as expected.
Or, if you do not want to use Layouts everywhere, I could check if we can use some custom code, but as said, it's the general purpose of Layouts to be "used everywhere or not at all".
This sounds scary, but it has it's reasons.
Please let me know, about the state of things, so we can proceed 🙂