Yes fr Spencer St: if there is one going to Hawthorn within 15min after you arrive take it. O/wise, to get to Flinders St, you just catch one of the many trains that go there.
I don't use public transport often, but I would assume it got better not worse since I last used the trains. It is pretty easy to figure out what's coming & going. You should also be able to see how long each train will take to reach particular stations. Just look at the electronic displays or ask the ticketmasters behind the glass.
