Jerusalem -> Masada -> Dead Sea only day trip or overnight

There are three alternatives for going to the Dead Sea:
1. One-day organised tour
2. Rent a car and go by yourself
3. Take public transport

Other than taking a dip in the sea, There are two main sites to see: Massada and the Ein Gedi Nature Reserve, and some smaller sites, e.g. Qumran. Massada is accessed by either the cable car or by climbing the snake path.

Looking at each alternative:
1. Only goes to Massada (via cable car), swim/spa and usually a visit to the Ahava cosmetic factory. You have the advantage of a tour guide and not worrying about driving, arrangements, meals, etc. Disadvantages - the usual problems with any organised tour; you also don't see Ein Gedi.
2. You can see what you want to see and you can do it all in one day if you get an early start (pick up the car the previous afternoon). Disadvantages - time wasted renting and returning car; dealing with traffic and directions.
3. Good choice if you want to go for only one day and see EITHER Massada or Ein Gedi. It gets a bit complicated and time-wasting if you want to see both because there is limited bus service connecting the two (you would need two days).

1 and 2 are the viable options for a short trip. The choice is yours.

Also note that it's not possible to do it by public transport in one day on a Friday or Saturday. Buses stop running at about 3 p.m. on Fridays and there are no buses on Saturdays.

You don't say when you are planning on doing this. Note that Friday April 13 is a religious holiday - the last day of Passover - and will be like a Saturday as far as public transport, lack of, is concerned, with services stopping in the afternoon of Thursday April 12.

And more on the same subject (you haven't given any indication of when you're planning this so it may not be relevant at all), car rental offices - except at the airport - are closed on Friday afternoons and Saturdays, and also on April 12-13 as above.

Is there camping available at Ein Gedi?