Some input would be great here is i have tried both, and they seem to work, however i am hoping someone who has alot of experiance in PDM will be able to advise.

Option 1

Use Parts and assemblies in there original "first" assemblies, and then any assemblies using these parts or sub assemblies then look at the first instance.

Option 2

All parts and sub assemblies are located in Parts, and sub assembly banks. and both (or more) aseemblies would then Shortcut to the parts bank.

Its really a question of should the original part or assembly be stored within a assembly or as a stand alone part?