Along with all the culture shock you may feel being in a foreign environment, using the train system can easily add another layer of stress while traveling in Japan. But worry not! Although it is new and may seem overwhelming, navigating through the train system in Japan is quite easy! Here's a guide on how to do it.
Mapping out your steps and planning your trip sounds obvious, but does wonders. Using a navigation app will save you time and show each step for you. For the purpose of this guide we'll be using "Japan Transit" which can be downloaded via iOS or Android.
To practice, let's take a trip to Osaka! Once you have the app running, list Hikone as "current location" and Osaka as "arriving destination". The app automatically lists information such as time, price, and transfers (if any). There is also an option to search for hotels in the area, if you'd like.
Now that we know where to go, we have to figure out how to go about it.

For a one-way ticket, first locate a ticket machine. Most have an English option, so you can use that if you're not comfortable with your Japanese abilities.
Most machines are set up in a way that your destination is named based off its price. Since we're going to Osaka we'd find the ticket option for the price we found on the app - we found our fare to be 1,980 yen. Pay, get your ticket, then head to the next step.
If you will be in Japan for longer than a couple of weeks, you might want to consider a reloadable train card instead of buying one-way tickets each time. All you have to do is insert your card into the ticket machine and load the card with however much credit you'd like. Some convienience stores even let you reload them there!

The next step is going through the ticket gate. They tend to be a series of back-to-back automated machines nearby the ticket kiosk. Lines for them move very quickly, so it can be intimidating at first!
If you have a one-way ticket, insert it into the slot. It will go through the machine and pop back up on the other side of the gates. Don't forget to grab it! You'll need it once you arrive at your destination.
If you're using a reloadable train card, just scan it on the reader and the doors will open up for you to pass through.
If you're struggling with the gates, don't be afraid to as the station attendants there. Many speak English, and even those that don't are always eager to help as best they can!
The most stressful part of your journey will be getting to the platform. With all the people rushing by and trains coming and going, it can get difficult to navigate. Fortunately, the app will list which platform you should head towards. If you don't know where to go, just ask a station attendant - they will either lead the way themselves or give you the number of the platform you should head off to.
Most station platforms have an electronic board that lists the most up-to-date information for the next couple of trains departing from that specific track. It will list what trains are incoming, what a few of the main stops on the line, and how soon the trains will arrive. It often cycles between Japanese and English depending on the station, but just in case it might be a good idea to know the kanji of your destination. Multiple lines can depart from the same platform, so make sure you get on the right one.

And that's all there is to it! If you don't have any transfers, you can sit back and enjoy the ride until you reach your destination. Don't forget about your one-way ticket if you have one as you'll need to insert it into the ticket gate in order to leave the station.
Have fun on your trip!