Currently, I'm pasting all of my markup AND content into the template, I then use TAGS and variables to create editable regions.
This is good, what you are doing already.
It is okay to paste markup in the content area.
What you are asking is design concept. You will see what best works for you when you are using your site more and more.
The template, as the name suggests should hold common items, items that will not be repeated.
This makes your life easier.
If you want to bake twenty cupcakes, you don't waste your time moulding them individually.
Get a template to do the cakes, shape-wise.
Any cakes with special design, will have to be done individually.