Hi there :-) I would suggest that you grab a map of the public transportation. It's worth it. From your hotel, you can get onto the Red Line (Inbound towards Alewife) and get off at Park St. This will pop you right smack dab at Boston Common, which (if I remember correctly) is the beginning of the trail. :-) To get to South Station, you would just go up Summer St. towards downtown (that's the easiest way to describe Boston. Walk towards the buildings or away from them. Haha.) You'll walk over a little bridge and past the Children's Museum and it'll be right there. It's by Summer St. and Atlantic Ave.
To get home, you have a few options, depending on where you stop. If your last stop is the Bunker Hill Monument, you can take the Community College T back (Orange Line-Inbound towards Forest Hills). Then you can either get off at Downtown Crossing and walk back to your hotel. Or if it's raining/you're exhausted, you can transfer to the Red line Outbound towards Mattapan or Braintree and get off at South Station.
For a cab, it's $2.25 for the first 1/8 of a mile and then $.30 for every other 1/8th of a mile. I'm not sure how many cabs there are in Charlestown though. I'd say to go for the T. It's really cheap/easy if you have good directions (which I'd like to think mine are pretty good haha). Here's a map of the freedom trail which shows the T-stops I mentioned and also a map of the T in general. Good luck and Cheers!
http://www.thefreedomtrail.org/maps/...on-nps-map.pdf
http://www.math.harvard.edu/location...bos_subway.png