t.references question regarding migrations..

Ok.. So I've been doing more reading after buying a few RoR books now.. I've got my data models setup without any foreign keys between the tables (much to my dismay).

What I'm wondering are the following :

1) should I be manually setting up the foreign keys by editing the initial migration     stuff to add the missing "t.references :my_cool_object" or should I be using the     scaffold generator for that when I create the 2nd and subsequent tables --? I'm     ordering the creation of the tables to ensure the initial tables are created first and     subsequent belongs_to and has_xxx are put in afterwards by hand -- I'm now     thinking I should probably have put xxx:references as part of the scaffold generation     line when building the secondary set of tables to ensure the proper "t:references"     were put in the migration area -- will that ensure my foreign keys are established     when I do the first "rake db::migrate"?

2) If I've got tailored changes in either of the model files or in the migrations area,     would the scaffolding blow those away if I re-do a piece of it from the command line?     (e.g. will I lose my belongs_to and has_one/many associations in the model files)?

3) Where can I find the available list of commands for the scaffold generator so I can make     proper use of it? I didn't see much in the full rails API docs but perhaps I overlooked it?

Thanks! I'm hoping I can put this data modeling behind me today and move on to the more entertaining parts (generating an app!).