Yes it is true that airlines travel company started charging money for having the privilege of choosing passenger seats for the cheapest flight ticket and that is not just one time fees for the entire journey. There is an extra charge for every time you change airplanes when you reach your transit point for layovers. For example: If you have stop over at three locations, the privilege of choosing seats will be charged three times because you will be changing airplanes each time you arrive at your stop over location in transit.
One of the advantages of checking in online and printing flight boarding pass online is that it helps you get through the physical check-in faster when you reach the airport, because you would have already received your airline boarding pass online printed out and you only need to check in your baggage physically afterwards. It sort of guarantee you a seat in the airplanes so that your economy flight tickets won't be given away to people in the flight tickets waiting list. At the time of your air tickets online check in, you can choose any available seats you want without any charge if it is only 24 hours before departure. Some International Airports has a different special line up area for people who had already checked in online.
To check in your flight online you will have to visit the flight airlines where you booked your air tickets. For example: if you booked your airline flight tickets to fly with jet airways, you will visit https://www.jetairways.com/EN/CA/planyourtravel/web-check-in.aspx
Once you are in the airline travel web page, you will enter in your flight booking information such as your flight departure city, first name, last name, PNR (Air tickets Booking reference number) and then click on "Check me in". If you don't know your flight booking reference number, you can ask your airline booking travel agent for the flight booking reference number. Or if you booked your airline tickets online, you can find the flight booking reference number printed somewhere in the flight booking confirmation pages.