hi.
1. when you start from workbench you deal with tables, rows.
after it you have to use reverse engineering for build schema.yml

2. when you start from schema.yml, you deal with objects here and after it 
you ask orm to build db based on this value-objects.

both cases have self benefits and self probs.

with 1-st case you can use some extended features of db.
here is few possible probs:
1. orm maybe don't support such features, as they are db specific
2. orm have another conventions about types (4ex boolean or enum types).
3. from 1-st and 2-nd no way to migrate smoothly to another db

with 2-nd case you can use features of orm and don't really care about how 
it was been saved/retrieved to db
here is probs too:
1. generated db probably not optimal, as it don't use any db specific 
features (4ex m-m relations have additional column id in ref table)
2. no way to work with structure of db in visual way

so i think it's matter of taste.
if you prefer to go in relational way (or you like to find&fix bugs in an 
orm), go with 1-st case.
if you prefer to go in object-oriented way(or you like to switch between 
sqlite-mysql-oracle based on day of week), go with 2-nd case.

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