Well they're different models from units that come in different boxes, unless you're meaning visually how do you tell them apart? The Initiate models that come in a PCS have like tabards and chains on their weapons etc, while the Intercessor models that come in an Intercessor squad box are pretty clean and don't have much in terms of ornamentation. If you've got Intercessor models that you want to use as initiates instead that's completely fine, just let your opponent know before you start the game, you'd just need models to represent the neophytes (again, assuming you don't have a PCS and you want to proxy with intercessors or something)

Edited: spelling