Sorry if this is a bit of an obvious question (I'm a bit slow :p), but what exactly do you mean by secondary route?
After the first prologue you can choose three routes, the lawyer, the police officer and the doctor. Depending on your choice you get different skills and meet some of the characters earlier etc. :) I am currently working on the lawyer route. All those routes happen in every playthrough, even if you don't choose to play them. The doctor happens after the lawyer route and the police officer route plays at the same time as both. :)
Hope that answers your question.