The order of elements in an EDD doesn't matter .. arrange them however you want. Alphabetically makes them easier to find later, but you can also group them by type (block vs. inline).
Your EDD is created based on your data model. You shouldn't generally start by creating an EDD from the ground up. This is the general process I'd follow ..
1) Define your data model based on the needed elements and structure/hierarchy of those elements
2) Create a DTD that defines that model (be sure to add any necessary attributes)
3) Generate an EDD from the DTD (in FM, choose StructureTools > New EDD, then StructureTools > Import DTD)
4) Now you can add context rules to the element definitions in the EDD to apply formatting, etc.
5) Import the EDD into a FM file that has the styles that are applied by the EDD (this becomes your template that is referenced by your structure application definition)
That should get you started ….
…scott