Here are some responses to your questions.
1. When creating a new table, it should create a new layout for you as well as the fields that you created. However, once you have created the initial table, any new fields that you create can be put on the layout automatically if first you have the option turned on and second if you are in layout mode on a layout that is based on a table occurrence of that base table. If you want to put fields on a layout which are not currently on there, you can choose your field tool and drag it to the layout. It will prompt you for which specific field.
2. Staying on the subject of table occurrences, a layout is based off a table occurrence. A table occurrence is based off a table. Simply deleting the table does not delete the table occurrence on the graph ( unless you choose that option when prompted ). Furthermore, deleting a table occurrence does not delete a layout. You have to delete the layout manually.
3. FileMaker by default does name the first table the same as your file name. You can rename this table if you wish as FileMaker uses its own ID system in the backend.
What you've said makes sense; I need to spend more time futzing around with the program. This is my first try at my own solution after going through an inventory-tracking mock db tutorial.