I am trying to customise my debut theme and am a bit stuck.
I am trying to create an alternate template for the template that shows all my products.
I am able to create an alternate collections.liquid and it also shows up in the admin an it all works fine. But my confusion is, this seems to be the same template for rendering the all my products (not just the products from that collection) too, but how/where select the alternate template for that in the admin?
In other words I am attempting to change the template for collections/all
By default the collections/all uses the collection.liquid file.
As you said you can create a new template collection.custom.liquid that you can use.
The interesting part is that there is no actual collection/all page in the admin. This is the default page that ALL shopify shops have (similar to the homepage/404/cart page). So you don't have access to it from the admin panel by default.
In order to change the ALL collection page you need to create it yourself. Go to your collections admin page and create a new collection with the handle all and this will overwrite the default all collection and you will be able to choose a different template for it.
TLDR; create a new "all" collection in the admin panel and choose the custom template for it.