Polish trains are not difficult. The internet has convinced you that they are. The internet, in this case, is wrong. What you need is forty minutes of reading and one app. Here is the whole thing, written by someone who takes them three times a week.
The one app you actually need
Install Koleo. That is it. Koleo aggregates every Polish carrier - PKP Intercity, Polregio, Koleje Małopolskie, the lot - into one timetable and one checkout. The official PKP app exists. Use Koleo.
Buy tickets in advance for IC and EIP trains. They get more expensive as the train fills, exactly like a flight. For local Polregio trains, you can buy on board or at the station - price is fixed.
Classes, explained in one paragraph
Second class is fine for anything under three hours. First class is worth the extra ten euros on anything over four hours, and is the right answer for Warsaw to Krakow if you want to work on the train. Premium class on EIP exists and is a marketing exercise.
The mistake everyone makes
If you buy a ticket and miss the train, the ticket is void. There is no “next train” grace period on long-distance routes. Local routes - Polregio, KML - usually let you ride the next one, but do not bet on it. Plan a thirty-minute buffer at the start of any day that involves a connection.
Validation
On some regional trains you must validate your ticket by stamping it in a yellow machine on the platform before boarding. If in doubt, stamp it. The fine for an unstamped valid ticket is not small.