I dont know what is the APL station. Are you talking about Santa Apolónia? If so, the majority of the time it doesnt matter because the train leaving Santa Apolonia stops in Oriente. It is just a matter of which one is closer or easier to get to.
There are only two trains that stop in Oriente but dont go through Santa Apolonia bc they are coming from Faro.
So, if you go to Oriente you will be able to catch any train going to Coimbra.
Regarding Coimbra, you have to get out in Coimbra-b (the train doesnt go to Coimbra-A) and then you get in another train to Coimbra A (dont need to buy another ticket) if you want to get closer to the center.